| anno_start anno_end anno_text entity_type sentence section | |
| 26 31 human species Structural diversity in a human antibody germline library TITLE | |
| 32 40 antibody protein_type Structural diversity in a human antibody germline library TITLE | |
| 11 19 antibody protein_type To support antibody therapeutic development, the crystal structures of a set of 16 germline variants composed of 4 different kappa light chains paired with 4 different heavy chains have been determined. ABSTRACT | |
| 49 67 crystal structures evidence To support antibody therapeutic development, the crystal structures of a set of 16 germline variants composed of 4 different kappa light chains paired with 4 different heavy chains have been determined. ABSTRACT | |
| 125 143 kappa light chains structure_element To support antibody therapeutic development, the crystal structures of a set of 16 germline variants composed of 4 different kappa light chains paired with 4 different heavy chains have been determined. ABSTRACT | |
| 168 180 heavy chains structure_element To support antibody therapeutic development, the crystal structures of a set of 16 germline variants composed of 4 different kappa light chains paired with 4 different heavy chains have been determined. ABSTRACT | |
| 9 21 heavy chains structure_element All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. ABSTRACT | |
| 29 54 antigen-binding fragments structure_element All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. ABSTRACT | |
| 56 60 Fabs structure_element All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. ABSTRACT | |
| 76 110 complementarity-determining region structure_element All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. ABSTRACT | |
| 112 115 CDR structure_element All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. ABSTRACT | |
| 117 119 H3 structure_element All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. ABSTRACT | |
| 152 155 Fab structure_element All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. ABSTRACT | |
| 156 165 structure evidence All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. ABSTRACT | |
| 4 22 structure analyses experimental_method The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. ABSTRACT | |
| 58 68 structures evidence The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. ABSTRACT | |
| 80 90 structures evidence The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. ABSTRACT | |
| 98 102 CDRs structure_element The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. ABSTRACT | |
| 111 116 VH:VL complex_assembly The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. ABSTRACT | |
| 117 137 packing interactions bond_interaction The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. ABSTRACT | |
| 4 7 CDR structure_element The CDR conformations for the most part are tightly clustered, especially for the ones with shorter lengths. ABSTRACT | |
| 4 10 longer protein_state The longer CDRs with tandem glycines or serines have more conformational diversity than the others. ABSTRACT | |
| 11 15 CDRs structure_element The longer CDRs with tandem glycines or serines have more conformational diversity than the others. ABSTRACT | |
| 28 36 glycines residue_name The longer CDRs with tandem glycines or serines have more conformational diversity than the others. ABSTRACT | |
| 40 47 serines residue_name The longer CDRs with tandem glycines or serines have more conformational diversity than the others. ABSTRACT | |
| 0 3 CDR structure_element CDR H3, despite having the same amino acid sequence, exhibits the largest conformational diversity. ABSTRACT | |
| 4 6 H3 structure_element CDR H3, despite having the same amino acid sequence, exhibits the largest conformational diversity. ABSTRACT | |
| 18 28 structures evidence About half of the structures have CDR H3 conformations similar to that of the parent; the others diverge significantly. ABSTRACT | |
| 34 37 CDR structure_element About half of the structures have CDR H3 conformations similar to that of the parent; the others diverge significantly. ABSTRACT | |
| 38 40 H3 structure_element About half of the structures have CDR H3 conformations similar to that of the parent; the others diverge significantly. ABSTRACT | |
| 27 30 CDR structure_element One conclusion is that the CDR H3 conformations are influenced by both their amino acid sequence and their structural environment determined by the heavy and light chain pairing. ABSTRACT | |
| 31 33 H3 structure_element One conclusion is that the CDR H3 conformations are influenced by both their amino acid sequence and their structural environment determined by the heavy and light chain pairing. ABSTRACT | |
| 148 153 heavy structure_element One conclusion is that the CDR H3 conformations are influenced by both their amino acid sequence and their structural environment determined by the heavy and light chain pairing. ABSTRACT | |
| 158 169 light chain structure_element One conclusion is that the CDR H3 conformations are influenced by both their amino acid sequence and their structural environment determined by the heavy and light chain pairing. ABSTRACT | |
| 4 16 stem regions structure_element The stem regions of 14 of the variant pairs are in the ‘kinked’ conformation, and only 2 are in the extended conformation. ABSTRACT | |
| 56 62 kinked protein_state The stem regions of 14 of the variant pairs are in the ‘kinked’ conformation, and only 2 are in the extended conformation. ABSTRACT | |
| 100 108 extended protein_state The stem regions of 14 of the variant pairs are in the ‘kinked’ conformation, and only 2 are in the extended conformation. ABSTRACT | |
| 19 21 VH structure_element The packing of the VH and VL domains is consistent with our knowledge of antibody structure, and the tilt angles between these domains cover a range of 11 degrees. ABSTRACT | |
| 26 28 VL structure_element The packing of the VH and VL domains is consistent with our knowledge of antibody structure, and the tilt angles between these domains cover a range of 11 degrees. ABSTRACT | |
| 73 81 antibody protein_type The packing of the VH and VL domains is consistent with our knowledge of antibody structure, and the tilt angles between these domains cover a range of 11 degrees. ABSTRACT | |
| 82 91 structure evidence The packing of the VH and VL domains is consistent with our knowledge of antibody structure, and the tilt angles between these domains cover a range of 11 degrees. ABSTRACT | |
| 101 112 tilt angles evidence The packing of the VH and VL domains is consistent with our knowledge of antibody structure, and the tilt angles between these domains cover a range of 11 degrees. ABSTRACT | |
| 10 20 structures evidence Two of 16 structures showed particularly large variations in the tilt angles when compared with the other pairings. ABSTRACT | |
| 65 76 tilt angles evidence Two of 16 structures showed particularly large variations in the tilt angles when compared with the other pairings. ABSTRACT | |
| 4 14 structures evidence The structures and their analyses provide a rich foundation for future antibody modeling and engineering efforts. ABSTRACT | |
| 71 79 antibody protein_type The structures and their analyses provide a rich foundation for future antibody modeling and engineering efforts. ABSTRACT | |
| 24 34 antibodies protein_type At present, therapeutic antibodies are the largest class of biotherapeutic proteins that are in clinical trials. INTRO | |
| 22 32 antibodies protein_type The use of monoclonal antibodies as therapeutics began in the early 1980s, and their composition has transitioned from murine antibodies to generally less immunogenic humanized and human antibodies. INTRO | |
| 119 125 murine taxonomy_domain The use of monoclonal antibodies as therapeutics began in the early 1980s, and their composition has transitioned from murine antibodies to generally less immunogenic humanized and human antibodies. INTRO | |
| 126 136 antibodies protein_type The use of monoclonal antibodies as therapeutics began in the early 1980s, and their composition has transitioned from murine antibodies to generally less immunogenic humanized and human antibodies. INTRO | |
| 181 186 human species The use of monoclonal antibodies as therapeutics began in the early 1980s, and their composition has transitioned from murine antibodies to generally less immunogenic humanized and human antibodies. INTRO | |
| 187 197 antibodies protein_type The use of monoclonal antibodies as therapeutics began in the early 1980s, and their composition has transitioned from murine antibodies to generally less immunogenic humanized and human antibodies. INTRO | |
| 42 47 human species The technologies currently used to obtain human antibodies include transgenic mice containing human antibody repertoires, cloning directly from human B cells, and in vitro selection from antibody libraries using various display technologies. INTRO | |
| 48 58 antibodies protein_type The technologies currently used to obtain human antibodies include transgenic mice containing human antibody repertoires, cloning directly from human B cells, and in vitro selection from antibody libraries using various display technologies. INTRO | |
| 78 82 mice taxonomy_domain The technologies currently used to obtain human antibodies include transgenic mice containing human antibody repertoires, cloning directly from human B cells, and in vitro selection from antibody libraries using various display technologies. INTRO | |
| 94 99 human species The technologies currently used to obtain human antibodies include transgenic mice containing human antibody repertoires, cloning directly from human B cells, and in vitro selection from antibody libraries using various display technologies. INTRO | |
| 100 108 antibody protein_type The technologies currently used to obtain human antibodies include transgenic mice containing human antibody repertoires, cloning directly from human B cells, and in vitro selection from antibody libraries using various display technologies. INTRO | |
| 144 149 human species The technologies currently used to obtain human antibodies include transgenic mice containing human antibody repertoires, cloning directly from human B cells, and in vitro selection from antibody libraries using various display technologies. INTRO | |
| 163 181 in vitro selection experimental_method The technologies currently used to obtain human antibodies include transgenic mice containing human antibody repertoires, cloning directly from human B cells, and in vitro selection from antibody libraries using various display technologies. INTRO | |
| 187 205 antibody libraries experimental_method The technologies currently used to obtain human antibodies include transgenic mice containing human antibody repertoires, cloning directly from human B cells, and in vitro selection from antibody libraries using various display technologies. INTRO | |
| 17 25 antibody protein_type Once a candidate antibody is identified, protein engineering is usually required to produce a molecule with the right biophysical and functional properties. INTRO | |
| 41 60 protein engineering experimental_method Once a candidate antibody is identified, protein engineering is usually required to produce a molecule with the right biophysical and functional properties. INTRO | |
| 63 80 atomic structures evidence All engineering efforts are guided by our understanding of the atomic structures of antibodies. INTRO | |
| 84 94 antibodies protein_type All engineering efforts are guided by our understanding of the atomic structures of antibodies. INTRO | |
| 21 38 crystal structure evidence In such efforts, the crystal structure of the specific antibody may not be available, but modeling can be used to guide the engineering efforts. INTRO | |
| 55 63 antibody protein_type In such efforts, the crystal structure of the specific antibody may not be available, but modeling can be used to guide the engineering efforts. INTRO | |
| 8 16 antibody protein_type Today's antibody modeling approaches, which normally focus on the variable region, are being developed by the application of structural principles and insights that are evolving as our knowledge of antibody structures continues to expand. INTRO | |
| 66 81 variable region structure_element Today's antibody modeling approaches, which normally focus on the variable region, are being developed by the application of structural principles and insights that are evolving as our knowledge of antibody structures continues to expand. INTRO | |
| 198 206 antibody protein_type Today's antibody modeling approaches, which normally focus on the variable region, are being developed by the application of structural principles and insights that are evolving as our knowledge of antibody structures continues to expand. INTRO | |
| 207 217 structures evidence Today's antibody modeling approaches, which normally focus on the variable region, are being developed by the application of structural principles and insights that are evolving as our knowledge of antibody structures continues to expand. INTRO | |
| 36 46 antibodies protein_type Our current structural knowledge of antibodies is based on a multitude of studies that used many techniques to gain insight into the functional and structural properties of this class of macromolecule. INTRO | |
| 15 23 antibody protein_type Five different antibody isotypes occur, IgG, IgD, IgE, IgA and IgM, and each isotype has a unique role in the adaptive immune system. INTRO | |
| 40 43 IgG protein Five different antibody isotypes occur, IgG, IgD, IgE, IgA and IgM, and each isotype has a unique role in the adaptive immune system. INTRO | |
| 45 48 IgD protein Five different antibody isotypes occur, IgG, IgD, IgE, IgA and IgM, and each isotype has a unique role in the adaptive immune system. INTRO | |
| 50 53 IgE protein Five different antibody isotypes occur, IgG, IgD, IgE, IgA and IgM, and each isotype has a unique role in the adaptive immune system. INTRO | |
| 55 58 IgA protein Five different antibody isotypes occur, IgG, IgD, IgE, IgA and IgM, and each isotype has a unique role in the adaptive immune system. INTRO | |
| 63 66 IgM protein Five different antibody isotypes occur, IgG, IgD, IgE, IgA and IgM, and each isotype has a unique role in the adaptive immune system. INTRO | |
| 0 3 IgG protein IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 5 8 IgD protein IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 13 16 IgE protein IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 44 56 heavy chains structure_element IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 58 61 HCs structure_element IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 69 81 light chains structure_element IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 83 86 LCs structure_element IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 103 118 disulfide bonds ptm IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 126 129 IgA protein IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 134 137 IgM protein IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 175 185 antibodies protein_type IgG, IgD and IgE isotypes are composed of 2 heavy chains (HCs) and 2 light chains (LCs) linked through disulfide bonds, while IgA and IgM are double and quintuple versions of antibodies, respectively. INTRO | |
| 9 12 IgG protein Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 14 17 IgD protein Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 22 25 IgA protein Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 51 59 variable structure_element Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 61 62 V structure_element Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 70 78 constant structure_element Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 80 81 C structure_element Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 98 101 IgE protein Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 106 109 IgM protein Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 164 172 C domain structure_element Isotypes IgG, IgD and IgA each have 4 domains, one variable (V) and 3 constant (C) domains, while IgE and IgM each have the same 4 domains along with an additional C domain. INTRO | |
| 53 54 J structure_element These multimeric forms are linked with an additional J chain. INTRO | |
| 4 7 LCs structure_element The LCs that associate with the HCs are divided into 2 functionally indistinguishable classes, κ and λ. INTRO | |
| 32 35 HCs structure_element The LCs that associate with the HCs are divided into 2 functionally indistinguishable classes, κ and λ. INTRO | |
| 95 96 κ structure_element The LCs that associate with the HCs are divided into 2 functionally indistinguishable classes, κ and λ. INTRO | |
| 101 102 λ structure_element The LCs that associate with the HCs are divided into 2 functionally indistinguishable classes, κ and λ. INTRO | |
| 5 6 κ structure_element Both κ and λ polypeptide chains are composed of a single V domain and a single C domain. INTRO | |
| 11 12 λ structure_element Both κ and λ polypeptide chains are composed of a single V domain and a single C domain. INTRO | |
| 57 65 V domain structure_element Both κ and λ polypeptide chains are composed of a single V domain and a single C domain. INTRO | |
| 79 87 C domain structure_element Both κ and λ polypeptide chains are composed of a single V domain and a single C domain. INTRO | |
| 4 9 heavy structure_element The heavy and light chains are composed of structural domains that have ∼110 amino acid residues. INTRO | |
| 14 26 light chains structure_element The heavy and light chains are composed of structural domains that have ∼110 amino acid residues. INTRO | |
| 43 61 structural domains structure_element The heavy and light chains are composed of structural domains that have ∼110 amino acid residues. INTRO | |
| 72 96 ∼110 amino acid residues residue_range The heavy and light chains are composed of structural domains that have ∼110 amino acid residues. INTRO | |
| 70 89 immunoglobulin fold structure_element These domains have a common folding pattern often referred to as the “immunoglobulin fold,” formed by the packing together of 2 anti-parallel β-sheets. INTRO | |
| 128 150 anti-parallel β-sheets structure_element These domains have a common folding pattern often referred to as the “immunoglobulin fold,” formed by the packing together of 2 anti-parallel β-sheets. INTRO | |
| 4 25 immunoglobulin chains protein_type All immunoglobulin chains have an N-terminal V domain followed by 1 to 4 C domains, depending upon the chain type. INTRO | |
| 45 53 V domain structure_element All immunoglobulin chains have an N-terminal V domain followed by 1 to 4 C domains, depending upon the chain type. INTRO | |
| 73 82 C domains structure_element All immunoglobulin chains have an N-terminal V domain followed by 1 to 4 C domains, depending upon the chain type. INTRO | |
| 3 13 antibodies protein_type In antibodies, the heavy and light chain V domains pack together forming the antigen combining site. INTRO | |
| 19 40 heavy and light chain structure_element In antibodies, the heavy and light chain V domains pack together forming the antigen combining site. INTRO | |
| 41 50 V domains structure_element In antibodies, the heavy and light chain V domains pack together forming the antigen combining site. INTRO | |
| 77 99 antigen combining site site In antibodies, the heavy and light chain V domains pack together forming the antigen combining site. INTRO | |
| 81 89 antibody protein_type This site, which interacts with the antigen (or target), is the focus of current antibody modeling efforts. INTRO | |
| 5 21 interaction site site This interaction site is composed of 6 complementarity-determining regions (CDRs) that were identified in early antibody amino acid sequence analyses to be hypervariable in nature, and thus are responsible for the sequence and structural diversity of our antibody repertoire. INTRO | |
| 39 74 complementarity-determining regions structure_element This interaction site is composed of 6 complementarity-determining regions (CDRs) that were identified in early antibody amino acid sequence analyses to be hypervariable in nature, and thus are responsible for the sequence and structural diversity of our antibody repertoire. INTRO | |
| 76 80 CDRs structure_element This interaction site is composed of 6 complementarity-determining regions (CDRs) that were identified in early antibody amino acid sequence analyses to be hypervariable in nature, and thus are responsible for the sequence and structural diversity of our antibody repertoire. INTRO | |
| 112 149 antibody amino acid sequence analyses experimental_method This interaction site is composed of 6 complementarity-determining regions (CDRs) that were identified in early antibody amino acid sequence analyses to be hypervariable in nature, and thus are responsible for the sequence and structural diversity of our antibody repertoire. INTRO | |
| 156 169 hypervariable protein_state This interaction site is composed of 6 complementarity-determining regions (CDRs) that were identified in early antibody amino acid sequence analyses to be hypervariable in nature, and thus are responsible for the sequence and structural diversity of our antibody repertoire. INTRO | |
| 255 263 antibody protein_type This interaction site is composed of 6 complementarity-determining regions (CDRs) that were identified in early antibody amino acid sequence analyses to be hypervariable in nature, and thus are responsible for the sequence and structural diversity of our antibody repertoire. INTRO | |
| 30 41 CDR regions structure_element The sequence diversity of the CDR regions presents a substantial challenge to antibody modeling. INTRO | |
| 78 86 antibody protein_type The sequence diversity of the CDR regions presents a substantial challenge to antibody modeling. INTRO | |
| 20 39 structural analysis experimental_method However, an initial structural analysis of the combining sites of the small set of structures of immunoglobulin fragments available in the 1980s found that 5 of the 6 hypervariable loops or CDRs had canonical structures (a limited set of main-chain conformations). INTRO | |
| 47 62 combining sites site However, an initial structural analysis of the combining sites of the small set of structures of immunoglobulin fragments available in the 1980s found that 5 of the 6 hypervariable loops or CDRs had canonical structures (a limited set of main-chain conformations). INTRO | |
| 83 93 structures evidence However, an initial structural analysis of the combining sites of the small set of structures of immunoglobulin fragments available in the 1980s found that 5 of the 6 hypervariable loops or CDRs had canonical structures (a limited set of main-chain conformations). INTRO | |
| 167 186 hypervariable loops structure_element However, an initial structural analysis of the combining sites of the small set of structures of immunoglobulin fragments available in the 1980s found that 5 of the 6 hypervariable loops or CDRs had canonical structures (a limited set of main-chain conformations). INTRO | |
| 190 194 CDRs structure_element However, an initial structural analysis of the combining sites of the small set of structures of immunoglobulin fragments available in the 1980s found that 5 of the 6 hypervariable loops or CDRs had canonical structures (a limited set of main-chain conformations). INTRO | |
| 2 5 CDR structure_element A CDR canonical structure is defined by its length and conserved residues located in the hypervariable loop and framework residues (V-region residues that are not part of the CDRs). INTRO | |
| 89 107 hypervariable loop structure_element A CDR canonical structure is defined by its length and conserved residues located in the hypervariable loop and framework residues (V-region residues that are not part of the CDRs). INTRO | |
| 112 130 framework residues structure_element A CDR canonical structure is defined by its length and conserved residues located in the hypervariable loop and framework residues (V-region residues that are not part of the CDRs). INTRO | |
| 132 140 V-region structure_element A CDR canonical structure is defined by its length and conserved residues located in the hypervariable loop and framework residues (V-region residues that are not part of the CDRs). INTRO | |
| 175 179 CDRs structure_element A CDR canonical structure is defined by its length and conserved residues located in the hypervariable loop and framework residues (V-region residues that are not part of the CDRs). INTRO | |
| 24 32 antibody protein_type Furthermore, studies of antibody sequences revealed that the total number of canonical structures are limited for each CDR, indicating possibly that antigen recognition may be affected by structural restrictions at the antigen-binding site. INTRO | |
| 119 122 CDR structure_element Furthermore, studies of antibody sequences revealed that the total number of canonical structures are limited for each CDR, indicating possibly that antigen recognition may be affected by structural restrictions at the antigen-binding site. INTRO | |
| 219 239 antigen-binding site site Furthermore, studies of antibody sequences revealed that the total number of canonical structures are limited for each CDR, indicating possibly that antigen recognition may be affected by structural restrictions at the antigen-binding site. INTRO | |
| 29 37 CDR loop structure_element Later studies found that the CDR loop length is the primary determining factor of antigen-binding site topography because it is the primary factor for determining a canonical structure. INTRO | |
| 82 102 antigen-binding site site Later studies found that the CDR loop length is the primary determining factor of antigen-binding site topography because it is the primary factor for determining a canonical structure. INTRO | |
| 66 68 LC structure_element Additional efforts have led to our current understanding that the LC CDRs L1, L2, and L3 have preferred sets of canonical structures based on length and amino acid sequence composition. INTRO | |
| 69 73 CDRs structure_element Additional efforts have led to our current understanding that the LC CDRs L1, L2, and L3 have preferred sets of canonical structures based on length and amino acid sequence composition. INTRO | |
| 74 76 L1 structure_element Additional efforts have led to our current understanding that the LC CDRs L1, L2, and L3 have preferred sets of canonical structures based on length and amino acid sequence composition. INTRO | |
| 78 80 L2 structure_element Additional efforts have led to our current understanding that the LC CDRs L1, L2, and L3 have preferred sets of canonical structures based on length and amino acid sequence composition. INTRO | |
| 86 88 L3 structure_element Additional efforts have led to our current understanding that the LC CDRs L1, L2, and L3 have preferred sets of canonical structures based on length and amino acid sequence composition. INTRO | |
| 43 45 H1 structure_element This was also found to be the case for the H1 and H2 CDRs. INTRO | |
| 50 52 H2 structure_element This was also found to be the case for the H1 and H2 CDRs. INTRO | |
| 53 57 CDRs structure_element This was also found to be the case for the H1 and H2 CDRs. INTRO | |
| 63 67 CDRs structure_element Classification schemes for the canonical structures of these 5 CDRs have emerged and evolved as the number of depositions in the Protein Data Bank of Fab fragments of antibodies grow. INTRO | |
| 150 153 Fab structure_element Classification schemes for the canonical structures of these 5 CDRs have emerged and evolved as the number of depositions in the Protein Data Bank of Fab fragments of antibodies grow. INTRO | |
| 167 177 antibodies protein_type Classification schemes for the canonical structures of these 5 CDRs have emerged and evolved as the number of depositions in the Protein Data Bank of Fab fragments of antibodies grow. INTRO | |
| 26 29 CDR structure_element Recently, a comprehensive CDR classification scheme was reported identifying 72 clusters of conformations observed in antibody structures. INTRO | |
| 118 126 antibody protein_type Recently, a comprehensive CDR classification scheme was reported identifying 72 clusters of conformations observed in antibody structures. INTRO | |
| 127 137 structures evidence Recently, a comprehensive CDR classification scheme was reported identifying 72 clusters of conformations observed in antibody structures. INTRO | |
| 42 45 CDR structure_element The knowledge and predictability of these CDR canonical structures have greatly advanced antibody modeling efforts. INTRO | |
| 56 66 structures evidence The knowledge and predictability of these CDR canonical structures have greatly advanced antibody modeling efforts. INTRO | |
| 89 97 antibody protein_type The knowledge and predictability of these CDR canonical structures have greatly advanced antibody modeling efforts. INTRO | |
| 15 19 CDRs structure_element In contrast to CDRs L1, L2, L3, H1 and H2, no canonical structures have been observed for CDR H3, which is the most variable in length and amino acid sequence. INTRO | |
| 20 22 L1 structure_element In contrast to CDRs L1, L2, L3, H1 and H2, no canonical structures have been observed for CDR H3, which is the most variable in length and amino acid sequence. INTRO | |
| 24 26 L2 structure_element In contrast to CDRs L1, L2, L3, H1 and H2, no canonical structures have been observed for CDR H3, which is the most variable in length and amino acid sequence. INTRO | |
| 28 30 L3 structure_element In contrast to CDRs L1, L2, L3, H1 and H2, no canonical structures have been observed for CDR H3, which is the most variable in length and amino acid sequence. INTRO | |
| 32 34 H1 structure_element In contrast to CDRs L1, L2, L3, H1 and H2, no canonical structures have been observed for CDR H3, which is the most variable in length and amino acid sequence. INTRO | |
| 39 41 H2 structure_element In contrast to CDRs L1, L2, L3, H1 and H2, no canonical structures have been observed for CDR H3, which is the most variable in length and amino acid sequence. INTRO | |
| 56 66 structures evidence In contrast to CDRs L1, L2, L3, H1 and H2, no canonical structures have been observed for CDR H3, which is the most variable in length and amino acid sequence. INTRO | |
| 90 93 CDR structure_element In contrast to CDRs L1, L2, L3, H1 and H2, no canonical structures have been observed for CDR H3, which is the most variable in length and amino acid sequence. INTRO | |
| 94 96 H3 structure_element In contrast to CDRs L1, L2, L3, H1 and H2, no canonical structures have been observed for CDR H3, which is the most variable in length and amino acid sequence. INTRO | |
| 96 101 loops structure_element Some clustering of conformations was observed for the shortest lengths; however, for the longer loops, only the portions nearest the framework (torso, stem or anchor region) were found to have defined conformations. INTRO | |
| 133 142 framework structure_element Some clustering of conformations was observed for the shortest lengths; however, for the longer loops, only the portions nearest the framework (torso, stem or anchor region) were found to have defined conformations. INTRO | |
| 144 149 torso structure_element Some clustering of conformations was observed for the shortest lengths; however, for the longer loops, only the portions nearest the framework (torso, stem or anchor region) were found to have defined conformations. INTRO | |
| 151 155 stem structure_element Some clustering of conformations was observed for the shortest lengths; however, for the longer loops, only the portions nearest the framework (torso, stem or anchor region) were found to have defined conformations. INTRO | |
| 159 172 anchor region structure_element Some clustering of conformations was observed for the shortest lengths; however, for the longer loops, only the portions nearest the framework (torso, stem or anchor region) were found to have defined conformations. INTRO | |
| 7 19 torso region structure_element In the torso region, 2 primary groups could be identified, which led to sequence-based rules that can predict with some degree of reliability the conformation of the stem region. INTRO | |
| 166 177 stem region structure_element In the torso region, 2 primary groups could be identified, which led to sequence-based rules that can predict with some degree of reliability the conformation of the stem region. INTRO | |
| 5 11 kinked protein_state The “kinked” or “bulged” conformation is the most prevalent, but an “extended” or “non-bulged” conformation is also, but less frequently, observed. INTRO | |
| 17 23 bulged protein_state The “kinked” or “bulged” conformation is the most prevalent, but an “extended” or “non-bulged” conformation is also, but less frequently, observed. INTRO | |
| 69 77 extended protein_state The “kinked” or “bulged” conformation is the most prevalent, but an “extended” or “non-bulged” conformation is also, but less frequently, observed. INTRO | |
| 83 93 non-bulged protein_state The “kinked” or “bulged” conformation is the most prevalent, but an “extended” or “non-bulged” conformation is also, but less frequently, observed. INTRO | |
| 83 96 anchor region structure_element The cataloging and development of the rules for predicting the conformation of the anchor region of CDR H3 continue to be refined, producing new insight into the CDR H3 conformations and new tools for antibody engineering. INTRO | |
| 100 103 CDR structure_element The cataloging and development of the rules for predicting the conformation of the anchor region of CDR H3 continue to be refined, producing new insight into the CDR H3 conformations and new tools for antibody engineering. INTRO | |
| 104 106 H3 structure_element The cataloging and development of the rules for predicting the conformation of the anchor region of CDR H3 continue to be refined, producing new insight into the CDR H3 conformations and new tools for antibody engineering. INTRO | |
| 162 165 CDR structure_element The cataloging and development of the rules for predicting the conformation of the anchor region of CDR H3 continue to be refined, producing new insight into the CDR H3 conformations and new tools for antibody engineering. INTRO | |
| 166 168 H3 structure_element The cataloging and development of the rules for predicting the conformation of the anchor region of CDR H3 continue to be refined, producing new insight into the CDR H3 conformations and new tools for antibody engineering. INTRO | |
| 201 209 antibody protein_type The cataloging and development of the rules for predicting the conformation of the anchor region of CDR H3 continue to be refined, producing new insight into the CDR H3 conformations and new tools for antibody engineering. INTRO | |
| 8 16 antibody protein_type Current antibody modeling approaches take advantage of the most recent advances in homology modeling, the evolving understanding of the CDR canonical structures, the emerging rules for CDR H3 modeling and the growing body of antibody structural data available from the PDB. INTRO | |
| 83 100 homology modeling experimental_method Current antibody modeling approaches take advantage of the most recent advances in homology modeling, the evolving understanding of the CDR canonical structures, the emerging rules for CDR H3 modeling and the growing body of antibody structural data available from the PDB. INTRO | |
| 136 139 CDR structure_element Current antibody modeling approaches take advantage of the most recent advances in homology modeling, the evolving understanding of the CDR canonical structures, the emerging rules for CDR H3 modeling and the growing body of antibody structural data available from the PDB. INTRO | |
| 150 160 structures evidence Current antibody modeling approaches take advantage of the most recent advances in homology modeling, the evolving understanding of the CDR canonical structures, the emerging rules for CDR H3 modeling and the growing body of antibody structural data available from the PDB. INTRO | |
| 185 188 CDR structure_element Current antibody modeling approaches take advantage of the most recent advances in homology modeling, the evolving understanding of the CDR canonical structures, the emerging rules for CDR H3 modeling and the growing body of antibody structural data available from the PDB. INTRO | |
| 189 191 H3 structure_element Current antibody modeling approaches take advantage of the most recent advances in homology modeling, the evolving understanding of the CDR canonical structures, the emerging rules for CDR H3 modeling and the growing body of antibody structural data available from the PDB. INTRO | |
| 225 233 antibody protein_type Current antibody modeling approaches take advantage of the most recent advances in homology modeling, the evolving understanding of the CDR canonical structures, the emerging rules for CDR H3 modeling and the growing body of antibody structural data available from the PDB. INTRO | |
| 7 36 antibody modeling assessments experimental_method Recent antibody modeling assessments show continued improvement in the quality of the models being generated by a variety of modeling methods. INTRO | |
| 9 17 antibody protein_type Although antibody modeling is improving, the latest assessment revealed a number of challenges that need to be overcome to provide accurate 3-dimensional models of antibody V regions, including accuracies in the modeling of CDR H3. INTRO | |
| 164 172 antibody protein_type Although antibody modeling is improving, the latest assessment revealed a number of challenges that need to be overcome to provide accurate 3-dimensional models of antibody V regions, including accuracies in the modeling of CDR H3. INTRO | |
| 173 182 V regions structure_element Although antibody modeling is improving, the latest assessment revealed a number of challenges that need to be overcome to provide accurate 3-dimensional models of antibody V regions, including accuracies in the modeling of CDR H3. INTRO | |
| 224 227 CDR structure_element Although antibody modeling is improving, the latest assessment revealed a number of challenges that need to be overcome to provide accurate 3-dimensional models of antibody V regions, including accuracies in the modeling of CDR H3. INTRO | |
| 228 230 H3 structure_element Although antibody modeling is improving, the latest assessment revealed a number of challenges that need to be overcome to provide accurate 3-dimensional models of antibody V regions, including accuracies in the modeling of CDR H3. INTRO | |
| 137 145 antibody protein_type The need for improvement in this area was also highlighted in a recent study reporting an approach and results that may influence future antibody modeling efforts. INTRO | |
| 29 58 antibody modeling assessments experimental_method One important finding of the antibody modeling assessments was that errors in the structural templates that are used as the basis for homology models can propagate into the final models, producing inaccuracies that may negatively influence the predictive nature of the V region model. INTRO | |
| 134 149 homology models experimental_method One important finding of the antibody modeling assessments was that errors in the structural templates that are used as the basis for homology models can propagate into the final models, producing inaccuracies that may negatively influence the predictive nature of the V region model. INTRO | |
| 269 277 V region structure_element One important finding of the antibody modeling assessments was that errors in the structural templates that are used as the basis for homology models can propagate into the final models, producing inaccuracies that may negatively influence the predictive nature of the V region model. INTRO | |
| 11 19 antibody protein_type To support antibody engineering and therapeutic development efforts, a phage library was designed and constructed based on a limited number of scaffolds built with frequently used human germ-line IGV and IGJ gene segments that encode antigen combining sites suitable for recognition of peptides and proteins. INTRO | |
| 71 84 phage library experimental_method To support antibody engineering and therapeutic development efforts, a phage library was designed and constructed based on a limited number of scaffolds built with frequently used human germ-line IGV and IGJ gene segments that encode antigen combining sites suitable for recognition of peptides and proteins. INTRO | |
| 180 185 human species To support antibody engineering and therapeutic development efforts, a phage library was designed and constructed based on a limited number of scaffolds built with frequently used human germ-line IGV and IGJ gene segments that encode antigen combining sites suitable for recognition of peptides and proteins. INTRO | |
| 196 199 IGV structure_element To support antibody engineering and therapeutic development efforts, a phage library was designed and constructed based on a limited number of scaffolds built with frequently used human germ-line IGV and IGJ gene segments that encode antigen combining sites suitable for recognition of peptides and proteins. INTRO | |
| 204 207 IGJ structure_element To support antibody engineering and therapeutic development efforts, a phage library was designed and constructed based on a limited number of scaffolds built with frequently used human germ-line IGV and IGJ gene segments that encode antigen combining sites suitable for recognition of peptides and proteins. INTRO | |
| 234 257 antigen combining sites site To support antibody engineering and therapeutic development efforts, a phage library was designed and constructed based on a limited number of scaffolds built with frequently used human germ-line IGV and IGJ gene segments that encode antigen combining sites suitable for recognition of peptides and proteins. INTRO | |
| 5 8 Fab structure_element This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 34 36 HC structure_element This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 48 56 IGHV1-69 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 58 63 H1-69 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 66 74 IGHV3-23 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 76 81 H3-23 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 87 95 IGHV5-51 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 96 101 H5-51 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 110 112 LC structure_element This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 128 129 κ structure_element This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 132 140 IGKV1-39 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 142 147 L1-39 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 150 158 IGKV3-11 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 160 165 L3-11 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 168 176 IGKV3-20 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 178 183 L3-20 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 189 196 IGKV4-1 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 198 202 L4-1 mutant This Fab library is composed of 3 HC germlines, IGHV1-69 (H1-69), IGHV3-23 (H3-23) and IGHV5-51(H5-51), and 4 LC germlines (all κ), IGKV1-39 (L1-39), IGKV3-11 (L3-11), IGKV3-20 (L3-20) and IGKV4-1 (L4-1). INTRO | |
| 98 108 structures evidence Selection of these genes was based on the high frequency of their use and their cognate canonical structures that were found binding to peptides and proteins, as well as their ability to be expressed in bacteria and displayed on filamentous phage. INTRO | |
| 190 211 expressed in bacteria experimental_method Selection of these genes was based on the high frequency of their use and their cognate canonical structures that were found binding to peptides and proteins, as well as their ability to be expressed in bacteria and displayed on filamentous phage. INTRO | |
| 216 246 displayed on filamentous phage experimental_method Selection of these genes was based on the high frequency of their use and their cognate canonical structures that were found binding to peptides and proteins, as well as their ability to be expressed in bacteria and displayed on filamentous phage. INTRO | |
| 70 75 human species The implementation of the library involves the diversification of the human germline genes to mimic that found in natural human libraries. INTRO | |
| 122 127 human species The implementation of the library involves the diversification of the human germline genes to mimic that found in natural human libraries. INTRO | |
| 4 36 crystal structure determinations experimental_method The crystal structure determinations and structural analyses of all germline Fabs in the library described above along with the structures of a fourth HC germline, IGHV3-53 (H3-53), paired with the 4 LCs of the library have been carried out to support antibody therapeutic development. INTRO | |
| 41 60 structural analyses experimental_method The crystal structure determinations and structural analyses of all germline Fabs in the library described above along with the structures of a fourth HC germline, IGHV3-53 (H3-53), paired with the 4 LCs of the library have been carried out to support antibody therapeutic development. INTRO | |
| 77 81 Fabs structure_element The crystal structure determinations and structural analyses of all germline Fabs in the library described above along with the structures of a fourth HC germline, IGHV3-53 (H3-53), paired with the 4 LCs of the library have been carried out to support antibody therapeutic development. INTRO | |
| 128 138 structures evidence The crystal structure determinations and structural analyses of all germline Fabs in the library described above along with the structures of a fourth HC germline, IGHV3-53 (H3-53), paired with the 4 LCs of the library have been carried out to support antibody therapeutic development. INTRO | |
| 151 153 HC structure_element The crystal structure determinations and structural analyses of all germline Fabs in the library described above along with the structures of a fourth HC germline, IGHV3-53 (H3-53), paired with the 4 LCs of the library have been carried out to support antibody therapeutic development. INTRO | |
| 164 172 IGHV3-53 mutant The crystal structure determinations and structural analyses of all germline Fabs in the library described above along with the structures of a fourth HC germline, IGHV3-53 (H3-53), paired with the 4 LCs of the library have been carried out to support antibody therapeutic development. INTRO | |
| 174 179 H3-53 mutant The crystal structure determinations and structural analyses of all germline Fabs in the library described above along with the structures of a fourth HC germline, IGHV3-53 (H3-53), paired with the 4 LCs of the library have been carried out to support antibody therapeutic development. INTRO | |
| 200 203 LCs structure_element The crystal structure determinations and structural analyses of all germline Fabs in the library described above along with the structures of a fourth HC germline, IGHV3-53 (H3-53), paired with the 4 LCs of the library have been carried out to support antibody therapeutic development. INTRO | |
| 252 260 antibody protein_type The crystal structure determinations and structural analyses of all germline Fabs in the library described above along with the structures of a fourth HC germline, IGHV3-53 (H3-53), paired with the 4 LCs of the library have been carried out to support antibody therapeutic development. INTRO | |
| 7 10 HCs structure_element All 16 HCs of the Fabs have the same CDR H3 that was reported in an earlier Fab structure. INTRO | |
| 18 22 Fabs structure_element All 16 HCs of the Fabs have the same CDR H3 that was reported in an earlier Fab structure. INTRO | |
| 37 40 CDR structure_element All 16 HCs of the Fabs have the same CDR H3 that was reported in an earlier Fab structure. INTRO | |
| 41 43 H3 structure_element All 16 HCs of the Fabs have the same CDR H3 that was reported in an earlier Fab structure. INTRO | |
| 76 79 Fab structure_element All 16 HCs of the Fabs have the same CDR H3 that was reported in an earlier Fab structure. INTRO | |
| 80 89 structure evidence All 16 HCs of the Fabs have the same CDR H3 that was reported in an earlier Fab structure. INTRO | |
| 47 49 VH structure_element This is the first systematic study of the same VH and VL structures in the context of different pairings. INTRO | |
| 54 56 VL structure_element This is the first systematic study of the same VH and VL structures in the context of different pairings. INTRO | |
| 57 67 structures evidence This is the first systematic study of the same VH and VL structures in the context of different pairings. INTRO | |
| 58 68 structures evidence The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 80 90 structures evidence The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 98 100 L1 structure_element The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 102 104 L2 structure_element The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 106 108 L3 structure_element The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 110 112 H1 structure_element The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 117 119 H2 structure_element The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 120 124 CDRs structure_element The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 130 140 structures evidence The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 148 151 CDR structure_element The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 152 155 H3s structure_element The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 165 170 VH:VL complex_assembly The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 171 191 packing interactions bond_interaction The structure analyses include comparisons of the overall structures, canonical structures of the L1, L2, L3, H1 and H2 CDRs, the structures of all CDR H3s, and the VH:VL packing interactions. INTRO | |
| 4 14 structures evidence The structures and their analyses provide a foundation for future antibody engineering and structure determination efforts. INTRO | |
| 66 74 antibody protein_type The structures and their analyses provide a foundation for future antibody engineering and structure determination efforts. INTRO | |
| 0 18 Crystal structures evidence Crystal structures RESULTS | |
| 0 12 Crystal data evidence Crystal data, X-ray data, and refinement statistics. TABLE | |
| 14 24 X-ray data evidence Crystal data, X-ray data, and refinement statistics. TABLE | |
| 30 51 refinement statistics evidence Crystal data, X-ray data, and refinement statistics. TABLE | |
| 12 24 Crystal data evidence (Continued) Crystal data, X-ray data, and refinement statistics. TABLE | |
| 26 36 X-ray data evidence (Continued) Crystal data, X-ray data, and refinement statistics. TABLE | |
| 42 63 refinement statistics evidence (Continued) Crystal data, X-ray data, and refinement statistics. TABLE | |
| 12 24 Crystal data evidence (Continued) Crystal data, X-ray data, and refinement statistics. TABLE | |
| 26 36 X-ray data evidence (Continued) Crystal data, X-ray data, and refinement statistics. TABLE | |
| 42 63 refinement statistics evidence (Continued) Crystal data, X-ray data, and refinement statistics. TABLE | |
| 12 24 Crystal data evidence (Continued) Crystal data, X-ray data, and refinement statistics. TABLE | |
| 26 36 X-ray data evidence (Continued) Crystal data, X-ray data, and refinement statistics. TABLE | |
| 42 63 refinement statistics evidence (Continued) Crystal data, X-ray data, and refinement statistics. TABLE | |
| 4 22 crystal structures evidence The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 28 44 germline library experimental_method The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 60 64 Fabs structure_element The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 90 93 HCs structure_element The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 95 100 H1-69 mutant The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 102 107 H3-23 mutant The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 109 114 H3-53 mutant The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 119 124 H5-51 mutant The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 132 135 LCs structure_element The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 137 142 L1-39 mutant The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 144 149 L3-11 mutant The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 151 156 L3-20 mutant The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 161 165 L4-1 mutant The crystal structures of a germline library composed of 16 Fabs generated by combining 4 HCs (H1-69, H3-23, H3-53 and H5-51) and 4 LCs (L1-39, L3-11, L3-20 and L4-1) have been determined. RESULTS | |
| 4 7 Fab structure_element The Fab heavy and light chain sequences for the variants numbered according to Chothia are shown in Fig. S1. RESULTS | |
| 18 29 light chain structure_element The Fab heavy and light chain sequences for the variants numbered according to Chothia are shown in Fig. S1. RESULTS | |
| 19 22 HCs structure_element The four different HCs all have the same CDR H3 sequence, ARYDGIYGELDF. RESULTS | |
| 41 44 CDR structure_element The four different HCs all have the same CDR H3 sequence, ARYDGIYGELDF. RESULTS | |
| 45 47 H3 structure_element The four different HCs all have the same CDR H3 sequence, ARYDGIYGELDF. RESULTS | |
| 58 70 ARYDGIYGELDF structure_element The four different HCs all have the same CDR H3 sequence, ARYDGIYGELDF. RESULTS | |
| 0 15 Crystallization experimental_method Crystallization of the 16 Fabs was previously reported. RESULTS | |
| 26 30 Fabs structure_element Crystallization of the 16 Fabs was previously reported. RESULTS | |
| 18 26 crystals evidence Three sets of the crystals were isomorphous with nearly identical unit cells (Table 1). RESULTS | |
| 18 29 H3-23:L3-11 complex_assembly These include (1) H3-23:L3-11 and H3-23:L4-1 in P212121, (2) H3-53:L1-39, H3-53:L3-11 and H3-53:L3-20 in P6522, and (3) H5-51:L1-39, H5-51:L3-11 and H5-51:L3-20 in P212121. RESULTS | |
| 34 44 H3-23:L4-1 complex_assembly These include (1) H3-23:L3-11 and H3-23:L4-1 in P212121, (2) H3-53:L1-39, H3-53:L3-11 and H3-53:L3-20 in P6522, and (3) H5-51:L1-39, H5-51:L3-11 and H5-51:L3-20 in P212121. RESULTS | |
| 61 72 H3-53:L1-39 complex_assembly These include (1) H3-23:L3-11 and H3-23:L4-1 in P212121, (2) H3-53:L1-39, H3-53:L3-11 and H3-53:L3-20 in P6522, and (3) H5-51:L1-39, H5-51:L3-11 and H5-51:L3-20 in P212121. RESULTS | |
| 74 85 H3-53:L3-11 complex_assembly These include (1) H3-23:L3-11 and H3-23:L4-1 in P212121, (2) H3-53:L1-39, H3-53:L3-11 and H3-53:L3-20 in P6522, and (3) H5-51:L1-39, H5-51:L3-11 and H5-51:L3-20 in P212121. RESULTS | |
| 90 101 H3-53:L3-20 complex_assembly These include (1) H3-23:L3-11 and H3-23:L4-1 in P212121, (2) H3-53:L1-39, H3-53:L3-11 and H3-53:L3-20 in P6522, and (3) H5-51:L1-39, H5-51:L3-11 and H5-51:L3-20 in P212121. RESULTS | |
| 120 131 H5-51:L1-39 complex_assembly These include (1) H3-23:L3-11 and H3-23:L4-1 in P212121, (2) H3-53:L1-39, H3-53:L3-11 and H3-53:L3-20 in P6522, and (3) H5-51:L1-39, H5-51:L3-11 and H5-51:L3-20 in P212121. RESULTS | |
| 133 144 H5-51:L3-11 complex_assembly These include (1) H3-23:L3-11 and H3-23:L4-1 in P212121, (2) H3-53:L1-39, H3-53:L3-11 and H3-53:L3-20 in P6522, and (3) H5-51:L1-39, H5-51:L3-11 and H5-51:L3-20 in P212121. RESULTS | |
| 149 160 H5-51:L3-20 complex_assembly These include (1) H3-23:L3-11 and H3-23:L4-1 in P212121, (2) H3-53:L1-39, H3-53:L3-11 and H3-53:L3-20 in P6522, and (3) H5-51:L1-39, H5-51:L3-11 and H5-51:L3-20 in P212121. RESULTS | |
| 72 80 PEG 3350 chemical Variations occur in the pH (buffer) and the additives, and, in group 3, PEG 3350 is the precipitant for one variants while ammonium sulfate is the precipitant for the other two. RESULTS | |
| 123 139 ammonium sulfate chemical Variations occur in the pH (buffer) and the additives, and, in group 3, PEG 3350 is the precipitant for one variants while ammonium sulfate is the precipitant for the other two. RESULTS | |
| 22 35 crystal forms evidence The similarity in the crystal forms is attributed in part to cross-seeding using the microseed matrix screening for groups 2 and 3. RESULTS | |
| 85 111 microseed matrix screening experimental_method The similarity in the crystal forms is attributed in part to cross-seeding using the microseed matrix screening for groups 2 and 3. RESULTS | |
| 4 22 crystal structures evidence The crystal structures of the 16 Fabs have been determined at resolutions ranging from 3.3 Å to 1.65 Å (Table 1). RESULTS | |
| 33 37 Fabs structure_element The crystal structures of the 16 Fabs have been determined at resolutions ranging from 3.3 Å to 1.65 Å (Table 1). RESULTS | |
| 14 17 Fab structure_element The number of Fab molecules in the crystallographic asymmetric unit varies from 1 (for 12 Fabs) to 2 (for 4 Fabs). RESULTS | |
| 90 94 Fabs structure_element The number of Fab molecules in the crystallographic asymmetric unit varies from 1 (for 12 Fabs) to 2 (for 4 Fabs). RESULTS | |
| 108 112 Fabs structure_element The number of Fab molecules in the crystallographic asymmetric unit varies from 1 (for 12 Fabs) to 2 (for 4 Fabs). RESULTS | |
| 12 22 structures evidence Overall the structures are fairly complete, and, as can be expected, the models for the higher resolution structures are more complete than those for the lower resolution structures (Table S1). RESULTS | |
| 106 116 structures evidence Overall the structures are fairly complete, and, as can be expected, the models for the higher resolution structures are more complete than those for the lower resolution structures (Table S1). RESULTS | |
| 171 181 structures evidence Overall the structures are fairly complete, and, as can be expected, the models for the higher resolution structures are more complete than those for the lower resolution structures (Table S1). RESULTS | |
| 16 19 HCs structure_element Invariably, the HCs have more disorder than the LCs. RESULTS | |
| 30 38 disorder protein_state Invariably, the HCs have more disorder than the LCs. RESULTS | |
| 48 51 LCs structure_element Invariably, the HCs have more disorder than the LCs. RESULTS | |
| 8 10 LC structure_element For the LC, the disorder is observed at 2 of the C-terminal residues with few exceptions. RESULTS | |
| 16 24 disorder protein_state For the LC, the disorder is observed at 2 of the C-terminal residues with few exceptions. RESULTS | |
| 58 60 LC structure_element Apart from the C-terminus, only a few surface residues in LC are disordered. RESULTS | |
| 65 75 disordered protein_state Apart from the C-terminus, only a few surface residues in LC are disordered. RESULTS | |
| 4 7 HCs structure_element The HCs feature the largest number of disordered residues, with the lower resolution structures having the most. RESULTS | |
| 38 48 disordered protein_state The HCs feature the largest number of disordered residues, with the lower resolution structures having the most. RESULTS | |
| 85 95 structures evidence The HCs feature the largest number of disordered residues, with the lower resolution structures having the most. RESULTS | |
| 53 63 disordered protein_state The C-terminal residues including the 6xHis tags are disordered in all 16 structures. RESULTS | |
| 74 84 structures evidence The C-terminal residues including the 6xHis tags are disordered in all 16 structures. RESULTS | |
| 93 103 structures evidence In addition to these, 2 primary disordered stretches of residues are observed in a number of structures (Table S1). RESULTS | |
| 17 21 loop structure_element One involves the loop connecting the first 2 β-strands of the constant domain (in all Fabs except H3-23:L1-39, H3-23:L3-11 and H3-53:L1-39). RESULTS | |
| 45 54 β-strands structure_element One involves the loop connecting the first 2 β-strands of the constant domain (in all Fabs except H3-23:L1-39, H3-23:L3-11 and H3-53:L1-39). RESULTS | |
| 62 77 constant domain structure_element One involves the loop connecting the first 2 β-strands of the constant domain (in all Fabs except H3-23:L1-39, H3-23:L3-11 and H3-53:L1-39). RESULTS | |
| 86 90 Fabs structure_element One involves the loop connecting the first 2 β-strands of the constant domain (in all Fabs except H3-23:L1-39, H3-23:L3-11 and H3-53:L1-39). RESULTS | |
| 98 109 H3-23:L1-39 complex_assembly One involves the loop connecting the first 2 β-strands of the constant domain (in all Fabs except H3-23:L1-39, H3-23:L3-11 and H3-53:L1-39). RESULTS | |
| 111 122 H3-23:L3-11 complex_assembly One involves the loop connecting the first 2 β-strands of the constant domain (in all Fabs except H3-23:L1-39, H3-23:L3-11 and H3-53:L1-39). RESULTS | |
| 127 138 H3-53:L1-39 complex_assembly One involves the loop connecting the first 2 β-strands of the constant domain (in all Fabs except H3-23:L1-39, H3-23:L3-11 and H3-53:L1-39). RESULTS | |
| 24 27 CDR structure_element The other is located in CDR H3 (in H5-51:L3-11, H5-51:L3-20 and in one of 2 copies of H3-23:L4-1). RESULTS | |
| 28 30 H3 structure_element The other is located in CDR H3 (in H5-51:L3-11, H5-51:L3-20 and in one of 2 copies of H3-23:L4-1). RESULTS | |
| 35 46 H5-51:L3-11 complex_assembly The other is located in CDR H3 (in H5-51:L3-11, H5-51:L3-20 and in one of 2 copies of H3-23:L4-1). RESULTS | |
| 48 59 H5-51:L3-20 complex_assembly The other is located in CDR H3 (in H5-51:L3-11, H5-51:L3-20 and in one of 2 copies of H3-23:L4-1). RESULTS | |
| 86 96 H3-23:L4-1 complex_assembly The other is located in CDR H3 (in H5-51:L3-11, H5-51:L3-20 and in one of 2 copies of H3-23:L4-1). RESULTS | |
| 0 3 CDR structure_element CDR H1 and CDR H2 also show some degree of disorder, but to a lesser extent. RESULTS | |
| 4 6 H1 structure_element CDR H1 and CDR H2 also show some degree of disorder, but to a lesser extent. RESULTS | |
| 11 14 CDR structure_element CDR H1 and CDR H2 also show some degree of disorder, but to a lesser extent. RESULTS | |
| 15 17 H2 structure_element CDR H1 and CDR H2 also show some degree of disorder, but to a lesser extent. RESULTS | |
| 43 51 disorder protein_state CDR H1 and CDR H2 also show some degree of disorder, but to a lesser extent. RESULTS | |
| 0 3 CDR structure_element CDR canonical structures RESULTS | |
| 14 24 structures evidence CDR canonical structures RESULTS | |
| 8 11 CDR structure_element Several CDR definitions have evolved over decades of antibody research. RESULTS | |
| 53 61 antibody protein_type Several CDR definitions have evolved over decades of antibody research. RESULTS | |
| 41 44 CDR structure_element Depending on the focus of the study, the CDR boundaries differ slightly between various definitions. RESULTS | |
| 25 28 CDR structure_element In this work, we use the CDR definition of North et al., which is similar to that of Martin with the following exceptions: 1) CDRs H1 and H3 begin immediately after the Cys; and 2) CDR L2 includes an additional residue at the N-terminal side, typically Tyr. RESULTS | |
| 126 130 CDRs structure_element In this work, we use the CDR definition of North et al., which is similar to that of Martin with the following exceptions: 1) CDRs H1 and H3 begin immediately after the Cys; and 2) CDR L2 includes an additional residue at the N-terminal side, typically Tyr. RESULTS | |
| 131 133 H1 structure_element In this work, we use the CDR definition of North et al., which is similar to that of Martin with the following exceptions: 1) CDRs H1 and H3 begin immediately after the Cys; and 2) CDR L2 includes an additional residue at the N-terminal side, typically Tyr. RESULTS | |
| 138 140 H3 structure_element In this work, we use the CDR definition of North et al., which is similar to that of Martin with the following exceptions: 1) CDRs H1 and H3 begin immediately after the Cys; and 2) CDR L2 includes an additional residue at the N-terminal side, typically Tyr. RESULTS | |
| 169 172 Cys residue_name In this work, we use the CDR definition of North et al., which is similar to that of Martin with the following exceptions: 1) CDRs H1 and H3 begin immediately after the Cys; and 2) CDR L2 includes an additional residue at the N-terminal side, typically Tyr. RESULTS | |
| 181 184 CDR structure_element In this work, we use the CDR definition of North et al., which is similar to that of Martin with the following exceptions: 1) CDRs H1 and H3 begin immediately after the Cys; and 2) CDR L2 includes an additional residue at the N-terminal side, typically Tyr. RESULTS | |
| 185 187 L2 structure_element In this work, we use the CDR definition of North et al., which is similar to that of Martin with the following exceptions: 1) CDRs H1 and H3 begin immediately after the Cys; and 2) CDR L2 includes an additional residue at the N-terminal side, typically Tyr. RESULTS | |
| 253 256 Tyr residue_name In this work, we use the CDR definition of North et al., which is similar to that of Martin with the following exceptions: 1) CDRs H1 and H3 begin immediately after the Cys; and 2) CDR L2 includes an additional residue at the N-terminal side, typically Tyr. RESULTS | |
| 0 3 CDR structure_element CDR H1 RESULTS | |
| 4 6 H1 structure_element CDR H1 RESULTS | |
| 4 17 superposition experimental_method The superposition of CDR H1 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 21 24 CDR structure_element The superposition of CDR H1 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 25 27 H1 structure_element The superposition of CDR H1 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 46 51 HC:LC complex_assembly The superposition of CDR H1 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 63 75 heavy chains structure_element The superposition of CDR H1 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 81 86 H1-69 mutant The superposition of CDR H1 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 92 97 H3-23 mutant The superposition of CDR H1 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 103 108 H3-53 mutant The superposition of CDR H1 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 117 122 H5-51 mutant The superposition of CDR H1 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 0 4 CDRs structure_element CDRs are defined using the Dunbrack convention [12]. TABLE | |
| 32 35 Fab structure_element Assignments for 2 copies of the Fab in the asymmetric unit are given for 5 structures. TABLE | |
| 75 85 structures evidence Assignments for 2 copies of the Fab in the asymmetric unit are given for 5 structures. TABLE | |
| 23 27 CDRs structure_element No assignment (NA) for CDRs with missing residues. TABLE | |
| 9 12 HCs structure_element The four HCs feature CDR H1 of the same length, and their sequences are highly similar (Table 2). RESULTS | |
| 21 24 CDR structure_element The four HCs feature CDR H1 of the same length, and their sequences are highly similar (Table 2). RESULTS | |
| 25 27 H1 structure_element The four HCs feature CDR H1 of the same length, and their sequences are highly similar (Table 2). RESULTS | |
| 4 7 CDR structure_element The CDR H1 backbone conformations for all variants for each of the HCs are shown in Fig. 1. RESULTS | |
| 8 10 H1 structure_element The CDR H1 backbone conformations for all variants for each of the HCs are shown in Fig. 1. RESULTS | |
| 67 70 HCs structure_element The CDR H1 backbone conformations for all variants for each of the HCs are shown in Fig. 1. RESULTS | |
| 13 16 HCs structure_element Three of the HCs, H3-23, H3-53 and H5-51, have the same canonical structure, H1-13-1, and the backbone conformations are tightly clustered for each set of Fab structures as reflected in the rmsd values (Fig. 1B-D). RESULTS | |
| 18 23 H3-23 mutant Three of the HCs, H3-23, H3-53 and H5-51, have the same canonical structure, H1-13-1, and the backbone conformations are tightly clustered for each set of Fab structures as reflected in the rmsd values (Fig. 1B-D). RESULTS | |
| 25 30 H3-53 mutant Three of the HCs, H3-23, H3-53 and H5-51, have the same canonical structure, H1-13-1, and the backbone conformations are tightly clustered for each set of Fab structures as reflected in the rmsd values (Fig. 1B-D). RESULTS | |
| 35 40 H5-51 mutant Three of the HCs, H3-23, H3-53 and H5-51, have the same canonical structure, H1-13-1, and the backbone conformations are tightly clustered for each set of Fab structures as reflected in the rmsd values (Fig. 1B-D). RESULTS | |
| 77 84 H1-13-1 mutant Three of the HCs, H3-23, H3-53 and H5-51, have the same canonical structure, H1-13-1, and the backbone conformations are tightly clustered for each set of Fab structures as reflected in the rmsd values (Fig. 1B-D). RESULTS | |
| 155 158 Fab structure_element Three of the HCs, H3-23, H3-53 and H5-51, have the same canonical structure, H1-13-1, and the backbone conformations are tightly clustered for each set of Fab structures as reflected in the rmsd values (Fig. 1B-D). RESULTS | |
| 159 169 structures evidence Three of the HCs, H3-23, H3-53 and H5-51, have the same canonical structure, H1-13-1, and the backbone conformations are tightly clustered for each set of Fab structures as reflected in the rmsd values (Fig. 1B-D). RESULTS | |
| 190 201 rmsd values evidence Three of the HCs, H3-23, H3-53 and H5-51, have the same canonical structure, H1-13-1, and the backbone conformations are tightly clustered for each set of Fab structures as reflected in the rmsd values (Fig. 1B-D). RESULTS | |
| 31 36 H3-53 mutant Some deviation is observed for H3-53, mostly due to H3-53:L4-1, which exhibits a significant degree of disorder in CDR H1. RESULTS | |
| 52 62 H3-53:L4-1 complex_assembly Some deviation is observed for H3-53, mostly due to H3-53:L4-1, which exhibits a significant degree of disorder in CDR H1. RESULTS | |
| 115 118 CDR structure_element Some deviation is observed for H3-53, mostly due to H3-53:L4-1, which exhibits a significant degree of disorder in CDR H1. RESULTS | |
| 119 121 H1 structure_element Some deviation is observed for H3-53, mostly due to H3-53:L4-1, which exhibits a significant degree of disorder in CDR H1. RESULTS | |
| 4 20 electron density evidence The electron density for the backbone is weak and discontinuous, and completely missing for several side chains. RESULTS | |
| 4 7 CDR structure_element The CDR H1 structures with H1-69 shown in Fig. 1A are quite variable, both for the structures with different LCs and for the copies of the same Fab in the asymmetric unit, H1-69:L3-11 and H1-69:L3-20. RESULTS | |
| 8 10 H1 structure_element The CDR H1 structures with H1-69 shown in Fig. 1A are quite variable, both for the structures with different LCs and for the copies of the same Fab in the asymmetric unit, H1-69:L3-11 and H1-69:L3-20. RESULTS | |
| 11 21 structures evidence The CDR H1 structures with H1-69 shown in Fig. 1A are quite variable, both for the structures with different LCs and for the copies of the same Fab in the asymmetric unit, H1-69:L3-11 and H1-69:L3-20. RESULTS | |
| 27 32 H1-69 mutant The CDR H1 structures with H1-69 shown in Fig. 1A are quite variable, both for the structures with different LCs and for the copies of the same Fab in the asymmetric unit, H1-69:L3-11 and H1-69:L3-20. RESULTS | |
| 83 93 structures evidence The CDR H1 structures with H1-69 shown in Fig. 1A are quite variable, both for the structures with different LCs and for the copies of the same Fab in the asymmetric unit, H1-69:L3-11 and H1-69:L3-20. RESULTS | |
| 109 112 LCs structure_element The CDR H1 structures with H1-69 shown in Fig. 1A are quite variable, both for the structures with different LCs and for the copies of the same Fab in the asymmetric unit, H1-69:L3-11 and H1-69:L3-20. RESULTS | |
| 144 147 Fab structure_element The CDR H1 structures with H1-69 shown in Fig. 1A are quite variable, both for the structures with different LCs and for the copies of the same Fab in the asymmetric unit, H1-69:L3-11 and H1-69:L3-20. RESULTS | |
| 172 183 H1-69:L3-11 complex_assembly The CDR H1 structures with H1-69 shown in Fig. 1A are quite variable, both for the structures with different LCs and for the copies of the same Fab in the asymmetric unit, H1-69:L3-11 and H1-69:L3-20. RESULTS | |
| 188 199 H1-69:L3-20 complex_assembly The CDR H1 structures with H1-69 shown in Fig. 1A are quite variable, both for the structures with different LCs and for the copies of the same Fab in the asymmetric unit, H1-69:L3-11 and H1-69:L3-20. RESULTS | |
| 24 27 Fab structure_element In total, 6 independent Fab structures produce 5 different canonical structures, namely H1-13-1, H1-13-3, H1-13-4, H1-13-6 and H1-13-10. RESULTS | |
| 28 38 structures evidence In total, 6 independent Fab structures produce 5 different canonical structures, namely H1-13-1, H1-13-3, H1-13-4, H1-13-6 and H1-13-10. RESULTS | |
| 69 79 structures evidence In total, 6 independent Fab structures produce 5 different canonical structures, namely H1-13-1, H1-13-3, H1-13-4, H1-13-6 and H1-13-10. RESULTS | |
| 88 95 H1-13-1 mutant In total, 6 independent Fab structures produce 5 different canonical structures, namely H1-13-1, H1-13-3, H1-13-4, H1-13-6 and H1-13-10. RESULTS | |
| 97 104 H1-13-3 mutant In total, 6 independent Fab structures produce 5 different canonical structures, namely H1-13-1, H1-13-3, H1-13-4, H1-13-6 and H1-13-10. RESULTS | |
| 106 113 H1-13-4 mutant In total, 6 independent Fab structures produce 5 different canonical structures, namely H1-13-1, H1-13-3, H1-13-4, H1-13-6 and H1-13-10. RESULTS | |
| 115 122 H1-13-6 mutant In total, 6 independent Fab structures produce 5 different canonical structures, namely H1-13-1, H1-13-3, H1-13-4, H1-13-6 and H1-13-10. RESULTS | |
| 127 135 H1-13-10 mutant In total, 6 independent Fab structures produce 5 different canonical structures, namely H1-13-1, H1-13-3, H1-13-4, H1-13-6 and H1-13-10. RESULTS | |
| 22 27 H1-69 mutant A major difference of H1-69 from the other germlines in the experimental data set is the presence of Gly instead of Phe or Tyr at position 27 (residue 5 of 13 in CDR H1). RESULTS | |
| 101 104 Gly residue_name A major difference of H1-69 from the other germlines in the experimental data set is the presence of Gly instead of Phe or Tyr at position 27 (residue 5 of 13 in CDR H1). RESULTS | |
| 116 119 Phe residue_name A major difference of H1-69 from the other germlines in the experimental data set is the presence of Gly instead of Phe or Tyr at position 27 (residue 5 of 13 in CDR H1). RESULTS | |
| 123 126 Tyr residue_name A major difference of H1-69 from the other germlines in the experimental data set is the presence of Gly instead of Phe or Tyr at position 27 (residue 5 of 13 in CDR H1). RESULTS | |
| 139 141 27 residue_number A major difference of H1-69 from the other germlines in the experimental data set is the presence of Gly instead of Phe or Tyr at position 27 (residue 5 of 13 in CDR H1). RESULTS | |
| 162 165 CDR structure_element A major difference of H1-69 from the other germlines in the experimental data set is the presence of Gly instead of Phe or Tyr at position 27 (residue 5 of 13 in CDR H1). RESULTS | |
| 166 168 H1 structure_element A major difference of H1-69 from the other germlines in the experimental data set is the presence of Gly instead of Phe or Tyr at position 27 (residue 5 of 13 in CDR H1). RESULTS | |
| 0 7 Glycine residue_name Glycine introduces the possibility of a higher degree of conformational flexibility that undoubtedly translates to the differences observed, and contributes to the elevated thermal parameters for the atoms in the amino acid residues in this region. RESULTS | |
| 0 3 CDR structure_element CDR H2 RESULTS | |
| 4 6 H2 structure_element CDR H2 RESULTS | |
| 4 17 superposition experimental_method The superposition of CDR H2 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 21 24 CDR structure_element The superposition of CDR H2 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 25 27 H2 structure_element The superposition of CDR H2 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 46 51 HC:LC complex_assembly The superposition of CDR H2 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 63 75 heavy chains structure_element The superposition of CDR H2 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 81 86 H1-69 mutant The superposition of CDR H2 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 92 97 H3-23 mutant The superposition of CDR H2 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 103 108 H3-53 mutant The superposition of CDR H2 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 117 122 H5-51 mutant The superposition of CDR H2 backbones for all HC:LC pairs with heavy chains: (A) H1-69, (B) H3-23, (C) H3-53 and (D) H5-51. FIG | |
| 28 31 CDR structure_element The canonical structures of CDR H2 have fairly consistent conformations (Table 2, Fig. 2). RESULTS | |
| 32 34 H2 structure_element The canonical structures of CDR H2 have fairly consistent conformations (Table 2, Fig. 2). RESULTS | |
| 14 17 HCs structure_element Each of the 4 HCs adopts only one canonical structure regardless of the pairing LC. RESULTS | |
| 80 82 LC structure_element Each of the 4 HCs adopts only one canonical structure regardless of the pairing LC. RESULTS | |
| 10 15 H1-69 mutant Germlines H1-69 and H5-51 have the same canonical structure assignment H2-10-1, H3-23 has H2-10-2, and H3-53 has H2-9-3. RESULTS | |
| 20 25 H5-51 mutant Germlines H1-69 and H5-51 have the same canonical structure assignment H2-10-1, H3-23 has H2-10-2, and H3-53 has H2-9-3. RESULTS | |
| 71 78 H2-10-1 mutant Germlines H1-69 and H5-51 have the same canonical structure assignment H2-10-1, H3-23 has H2-10-2, and H3-53 has H2-9-3. RESULTS | |
| 80 85 H3-23 mutant Germlines H1-69 and H5-51 have the same canonical structure assignment H2-10-1, H3-23 has H2-10-2, and H3-53 has H2-9-3. RESULTS | |
| 90 97 H2-10-2 mutant Germlines H1-69 and H5-51 have the same canonical structure assignment H2-10-1, H3-23 has H2-10-2, and H3-53 has H2-9-3. RESULTS | |
| 103 108 H3-53 mutant Germlines H1-69 and H5-51 have the same canonical structure assignment H2-10-1, H3-23 has H2-10-2, and H3-53 has H2-9-3. RESULTS | |
| 113 119 H2-9-3 mutant Germlines H1-69 and H5-51 have the same canonical structure assignment H2-10-1, H3-23 has H2-10-2, and H3-53 has H2-9-3. RESULTS | |
| 35 38 CDR structure_element The conformations for all of these CDR H2s are tightly clustered (Fig. 2). RESULTS | |
| 39 42 H2s structure_element The conformations for all of these CDR H2s are tightly clustered (Fig. 2). RESULTS | |
| 27 30 Fab structure_element In one case, in the second Fab of H1-69:L3-20, CDR H2 is partially disordered (Δ55-60). RESULTS | |
| 34 45 H1-69:L3-20 complex_assembly In one case, in the second Fab of H1-69:L3-20, CDR H2 is partially disordered (Δ55-60). RESULTS | |
| 47 50 CDR structure_element In one case, in the second Fab of H1-69:L3-20, CDR H2 is partially disordered (Δ55-60). RESULTS | |
| 51 53 H2 structure_element In one case, in the second Fab of H1-69:L3-20, CDR H2 is partially disordered (Δ55-60). RESULTS | |
| 57 77 partially disordered protein_state In one case, in the second Fab of H1-69:L3-20, CDR H2 is partially disordered (Δ55-60). RESULTS | |
| 79 85 Δ55-60 mutant In one case, in the second Fab of H1-69:L3-20, CDR H2 is partially disordered (Δ55-60). RESULTS | |
| 37 40 CDR structure_element Although three of the germlines have CDR H2 of the same length, 10 residues, they adopt 2 distinctively different conformations depending mostly on the residue at position 71 from the so-called CDR H4. RESULTS | |
| 41 43 H2 structure_element Although three of the germlines have CDR H2 of the same length, 10 residues, they adopt 2 distinctively different conformations depending mostly on the residue at position 71 from the so-called CDR H4. RESULTS | |
| 64 75 10 residues residue_range Although three of the germlines have CDR H2 of the same length, 10 residues, they adopt 2 distinctively different conformations depending mostly on the residue at position 71 from the so-called CDR H4. RESULTS | |
| 172 174 71 residue_number Although three of the germlines have CDR H2 of the same length, 10 residues, they adopt 2 distinctively different conformations depending mostly on the residue at position 71 from the so-called CDR H4. RESULTS | |
| 194 197 CDR structure_element Although three of the germlines have CDR H2 of the same length, 10 residues, they adopt 2 distinctively different conformations depending mostly on the residue at position 71 from the so-called CDR H4. RESULTS | |
| 198 200 H4 structure_element Although three of the germlines have CDR H2 of the same length, 10 residues, they adopt 2 distinctively different conformations depending mostly on the residue at position 71 from the so-called CDR H4. RESULTS | |
| 0 5 Arg71 residue_name_number Arg71 in H3-23 fills the space between CDRs H2 and H4, and defines the conformation of the tip of CDR H2 so that residue 54 points away from the antigen binding site. RESULTS | |
| 9 14 H3-23 mutant Arg71 in H3-23 fills the space between CDRs H2 and H4, and defines the conformation of the tip of CDR H2 so that residue 54 points away from the antigen binding site. RESULTS | |
| 39 43 CDRs structure_element Arg71 in H3-23 fills the space between CDRs H2 and H4, and defines the conformation of the tip of CDR H2 so that residue 54 points away from the antigen binding site. RESULTS | |
| 44 46 H2 structure_element Arg71 in H3-23 fills the space between CDRs H2 and H4, and defines the conformation of the tip of CDR H2 so that residue 54 points away from the antigen binding site. RESULTS | |
| 51 53 H4 structure_element Arg71 in H3-23 fills the space between CDRs H2 and H4, and defines the conformation of the tip of CDR H2 so that residue 54 points away from the antigen binding site. RESULTS | |
| 98 101 CDR structure_element Arg71 in H3-23 fills the space between CDRs H2 and H4, and defines the conformation of the tip of CDR H2 so that residue 54 points away from the antigen binding site. RESULTS | |
| 102 104 H2 structure_element Arg71 in H3-23 fills the space between CDRs H2 and H4, and defines the conformation of the tip of CDR H2 so that residue 54 points away from the antigen binding site. RESULTS | |
| 121 123 54 residue_number Arg71 in H3-23 fills the space between CDRs H2 and H4, and defines the conformation of the tip of CDR H2 so that residue 54 points away from the antigen binding site. RESULTS | |
| 145 165 antigen binding site site Arg71 in H3-23 fills the space between CDRs H2 and H4, and defines the conformation of the tip of CDR H2 so that residue 54 points away from the antigen binding site. RESULTS | |
| 10 15 H1-69 mutant Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 20 25 H5-51 mutant Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 44 49 human species Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 74 77 Ala residue_name Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 90 92 71 residue_number Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 122 123 H structure_element Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 124 130 Pro52a residue_name_number Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 154 157 CDR structure_element Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 158 160 H4 structure_element Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 192 194 53 residue_number Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 199 201 54 residue_number Germlines H1-69 and H5-51 are unique in the human repertoire in having an Ala at position 71 that leaves enough space for H-Pro52a to pack deeper against CDR H4 so that the following residues 53 and 54 point toward the putative antigen. RESULTS | |
| 17 20 CDR structure_element Conformations of CDR H2 in H1-69 and H5-51, both of which have canonical structure H2-10-1, show little deviation within each set of 4 structures. RESULTS | |
| 21 23 H2 structure_element Conformations of CDR H2 in H1-69 and H5-51, both of which have canonical structure H2-10-1, show little deviation within each set of 4 structures. RESULTS | |
| 27 32 H1-69 mutant Conformations of CDR H2 in H1-69 and H5-51, both of which have canonical structure H2-10-1, show little deviation within each set of 4 structures. RESULTS | |
| 37 42 H5-51 mutant Conformations of CDR H2 in H1-69 and H5-51, both of which have canonical structure H2-10-1, show little deviation within each set of 4 structures. RESULTS | |
| 83 90 H2-10-1 mutant Conformations of CDR H2 in H1-69 and H5-51, both of which have canonical structure H2-10-1, show little deviation within each set of 4 structures. RESULTS | |
| 135 145 structures evidence Conformations of CDR H2 in H1-69 and H5-51, both of which have canonical structure H2-10-1, show little deviation within each set of 4 structures. RESULTS | |
| 45 48 CDR structure_element However, there is a significant shift of the CDR as a rigid body when the 2 sets are superimposed. RESULTS | |
| 85 97 superimposed experimental_method However, there is a significant shift of the CDR as a rigid body when the 2 sets are superimposed. RESULTS | |
| 49 52 CDR structure_element Most likely this is the result of interaction of CDR H2 with CDR H1, namely with the residue at position 33 (residue 11 of 13 in CDR H1). RESULTS | |
| 53 55 H2 structure_element Most likely this is the result of interaction of CDR H2 with CDR H1, namely with the residue at position 33 (residue 11 of 13 in CDR H1). RESULTS | |
| 61 64 CDR structure_element Most likely this is the result of interaction of CDR H2 with CDR H1, namely with the residue at position 33 (residue 11 of 13 in CDR H1). RESULTS | |
| 65 67 H1 structure_element Most likely this is the result of interaction of CDR H2 with CDR H1, namely with the residue at position 33 (residue 11 of 13 in CDR H1). RESULTS | |
| 105 107 33 residue_number Most likely this is the result of interaction of CDR H2 with CDR H1, namely with the residue at position 33 (residue 11 of 13 in CDR H1). RESULTS | |
| 129 132 CDR structure_element Most likely this is the result of interaction of CDR H2 with CDR H1, namely with the residue at position 33 (residue 11 of 13 in CDR H1). RESULTS | |
| 133 135 H1 structure_element Most likely this is the result of interaction of CDR H2 with CDR H1, namely with the residue at position 33 (residue 11 of 13 in CDR H1). RESULTS | |
| 9 14 H1-69 mutant Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 19 22 Ala residue_name Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 35 37 33 residue_number Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 49 54 H5-51 mutant Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 64 66 33 residue_number Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 90 93 Trp residue_name Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 116 117 H structure_element Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 118 123 Tyr52 residue_name_number Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 135 138 CDR structure_element Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 139 141 H2 structure_element Germline H1-69 has Ala at position 33 whereas in H5-51 position 33 is occupied by a bulky Trp, which stacks against H-Tyr52 and drives CDR H2 away from the center. RESULTS | |
| 0 3 CDR structure_element CDR L1 RESULTS | |
| 4 6 L1 structure_element CDR L1 RESULTS | |
| 4 17 superposition experimental_method The superposition of CDR L1 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 21 24 CDR structure_element The superposition of CDR L1 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 25 27 L1 structure_element The superposition of CDR L1 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 46 51 HC:LC complex_assembly The superposition of CDR L1 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 63 75 light chains structure_element The superposition of CDR L1 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 81 86 L1-39 mutant The superposition of CDR L1 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 92 97 L3-11 mutant The superposition of CDR L1 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 103 108 L3-20 mutant The superposition of CDR L1 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 117 121 L4-1 mutant The superposition of CDR L1 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 9 11 LC structure_element The four LC CDRs L1 feature 3 different lengths (11, 12 and 17 residues) having a total of 4 different canonical structure assignments. RESULTS | |
| 12 16 CDRs structure_element The four LC CDRs L1 feature 3 different lengths (11, 12 and 17 residues) having a total of 4 different canonical structure assignments. RESULTS | |
| 17 19 L1 structure_element The four LC CDRs L1 feature 3 different lengths (11, 12 and 17 residues) having a total of 4 different canonical structure assignments. RESULTS | |
| 49 51 11 residue_range The four LC CDRs L1 feature 3 different lengths (11, 12 and 17 residues) having a total of 4 different canonical structure assignments. RESULTS | |
| 53 55 12 residue_range The four LC CDRs L1 feature 3 different lengths (11, 12 and 17 residues) having a total of 4 different canonical structure assignments. RESULTS | |
| 60 62 17 residue_range The four LC CDRs L1 feature 3 different lengths (11, 12 and 17 residues) having a total of 4 different canonical structure assignments. RESULTS | |
| 9 12 LCs structure_element Of these LCs, L1-39 and L3-11 have the same canonical structure, L1-11-1, and superimpose very well (Fig. 3A, B). RESULTS | |
| 14 19 L1-39 mutant Of these LCs, L1-39 and L3-11 have the same canonical structure, L1-11-1, and superimpose very well (Fig. 3A, B). RESULTS | |
| 24 29 L3-11 mutant Of these LCs, L1-39 and L3-11 have the same canonical structure, L1-11-1, and superimpose very well (Fig. 3A, B). RESULTS | |
| 65 72 L1-11-1 mutant Of these LCs, L1-39 and L3-11 have the same canonical structure, L1-11-1, and superimpose very well (Fig. 3A, B). RESULTS | |
| 78 89 superimpose experimental_method Of these LCs, L1-39 and L3-11 have the same canonical structure, L1-11-1, and superimpose very well (Fig. 3A, B). RESULTS | |
| 21 26 L3-20 mutant For the remaining 2, L3-20 has 2 different assignments, L1-12-1 and L1-12-2, while L4-1 has a single assignment, L1-17-1. RESULTS | |
| 56 63 L1-12-1 mutant For the remaining 2, L3-20 has 2 different assignments, L1-12-1 and L1-12-2, while L4-1 has a single assignment, L1-17-1. RESULTS | |
| 68 75 L1-12-2 mutant For the remaining 2, L3-20 has 2 different assignments, L1-12-1 and L1-12-2, while L4-1 has a single assignment, L1-17-1. RESULTS | |
| 83 87 L4-1 mutant For the remaining 2, L3-20 has 2 different assignments, L1-12-1 and L1-12-2, while L4-1 has a single assignment, L1-17-1. RESULTS | |
| 113 120 L1-17-1 mutant For the remaining 2, L3-20 has 2 different assignments, L1-12-1 and L1-12-2, while L4-1 has a single assignment, L1-17-1. RESULTS | |
| 0 4 L4-1 mutant L4-1 has the longest CDR L1, composed of 17 amino acid residues (Fig. 3D). RESULTS | |
| 21 24 CDR structure_element L4-1 has the longest CDR L1, composed of 17 amino acid residues (Fig. 3D). RESULTS | |
| 25 27 L1 structure_element L4-1 has the longest CDR L1, composed of 17 amino acid residues (Fig. 3D). RESULTS | |
| 41 63 17 amino acid residues residue_range L4-1 has the longest CDR L1, composed of 17 amino acid residues (Fig. 3D). RESULTS | |
| 55 59 rmsd evidence Despite this, the conformations are tightly clustered (rmsd is 0.20 Å). RESULTS | |
| 34 46 stem regions structure_element The backbone conformations of the stem regions superimpose well. RESULTS | |
| 52 55 30a residue_number Some changes in conformation occur between residues 30a and 30f (residues 8 and 13 of 17 in CDR L1). RESULTS | |
| 60 63 30f residue_number Some changes in conformation occur between residues 30a and 30f (residues 8 and 13 of 17 in CDR L1). RESULTS | |
| 74 75 8 residue_number Some changes in conformation occur between residues 30a and 30f (residues 8 and 13 of 17 in CDR L1). RESULTS | |
| 80 82 13 residue_number Some changes in conformation occur between residues 30a and 30f (residues 8 and 13 of 17 in CDR L1). RESULTS | |
| 86 88 17 residue_number Some changes in conformation occur between residues 30a and 30f (residues 8 and 13 of 17 in CDR L1). RESULTS | |
| 92 95 CDR structure_element Some changes in conformation occur between residues 30a and 30f (residues 8 and 13 of 17 in CDR L1). RESULTS | |
| 96 98 L1 structure_element Some changes in conformation occur between residues 30a and 30f (residues 8 and 13 of 17 in CDR L1). RESULTS | |
| 23 34 loop region structure_element This is the tip of the loop region, which appears to have similar conformations that fan out the structures because of the slight differences in torsion angles in the backbone near Tyr30a and Lys30f. RESULTS | |
| 97 107 structures evidence This is the tip of the loop region, which appears to have similar conformations that fan out the structures because of the slight differences in torsion angles in the backbone near Tyr30a and Lys30f. RESULTS | |
| 181 187 Tyr30a residue_name_number This is the tip of the loop region, which appears to have similar conformations that fan out the structures because of the slight differences in torsion angles in the backbone near Tyr30a and Lys30f. RESULTS | |
| 192 198 Lys30f residue_name_number This is the tip of the loop region, which appears to have similar conformations that fan out the structures because of the slight differences in torsion angles in the backbone near Tyr30a and Lys30f. RESULTS | |
| 0 5 L3-20 mutant L3-20 is the most variable in CDR L1 among the 4 germlines as indicated by an rmsd of 0.54 Å (Fig. 3C). RESULTS | |
| 30 33 CDR structure_element L3-20 is the most variable in CDR L1 among the 4 germlines as indicated by an rmsd of 0.54 Å (Fig. 3C). RESULTS | |
| 34 36 L1 structure_element L3-20 is the most variable in CDR L1 among the 4 germlines as indicated by an rmsd of 0.54 Å (Fig. 3C). RESULTS | |
| 78 82 rmsd evidence L3-20 is the most variable in CDR L1 among the 4 germlines as indicated by an rmsd of 0.54 Å (Fig. 3C). RESULTS | |
| 4 14 structures evidence Two structures, H3-53:L3-20 and H5-51:L3-20 are assigned to canonical structure L1-12-1 with virtually identical backbone conformations. RESULTS | |
| 16 27 H3-53:L3-20 complex_assembly Two structures, H3-53:L3-20 and H5-51:L3-20 are assigned to canonical structure L1-12-1 with virtually identical backbone conformations. RESULTS | |
| 32 43 H5-51:L3-20 complex_assembly Two structures, H3-53:L3-20 and H5-51:L3-20 are assigned to canonical structure L1-12-1 with virtually identical backbone conformations. RESULTS | |
| 80 87 L1-12-1 mutant Two structures, H3-53:L3-20 and H5-51:L3-20 are assigned to canonical structure L1-12-1 with virtually identical backbone conformations. RESULTS | |
| 21 32 H3-23:L3-20 complex_assembly The third structure, H3-23:L3-20, has CDR L1 as L1-12-2, which deviates from L1-12-1 at residues 29-32, i.e., at the site of insertion with respect to the 11-residue CDR. RESULTS | |
| 38 41 CDR structure_element The third structure, H3-23:L3-20, has CDR L1 as L1-12-2, which deviates from L1-12-1 at residues 29-32, i.e., at the site of insertion with respect to the 11-residue CDR. RESULTS | |
| 42 44 L1 structure_element The third structure, H3-23:L3-20, has CDR L1 as L1-12-2, which deviates from L1-12-1 at residues 29-32, i.e., at the site of insertion with respect to the 11-residue CDR. RESULTS | |
| 48 55 L1-12-2 mutant The third structure, H3-23:L3-20, has CDR L1 as L1-12-2, which deviates from L1-12-1 at residues 29-32, i.e., at the site of insertion with respect to the 11-residue CDR. RESULTS | |
| 77 84 L1-12-1 mutant The third structure, H3-23:L3-20, has CDR L1 as L1-12-2, which deviates from L1-12-1 at residues 29-32, i.e., at the site of insertion with respect to the 11-residue CDR. RESULTS | |
| 97 102 29-32 residue_range The third structure, H3-23:L3-20, has CDR L1 as L1-12-2, which deviates from L1-12-1 at residues 29-32, i.e., at the site of insertion with respect to the 11-residue CDR. RESULTS | |
| 155 165 11-residue residue_range The third structure, H3-23:L3-20, has CDR L1 as L1-12-2, which deviates from L1-12-1 at residues 29-32, i.e., at the site of insertion with respect to the 11-residue CDR. RESULTS | |
| 166 169 CDR structure_element The third structure, H3-23:L3-20, has CDR L1 as L1-12-2, which deviates from L1-12-1 at residues 29-32, i.e., at the site of insertion with respect to the 11-residue CDR. RESULTS | |
| 30 41 H1-69:L3-20 complex_assembly The fourth member of the set, H1-69:L3-20, was crystallized with 2 Fabs in the asymmetric unit. RESULTS | |
| 47 59 crystallized experimental_method The fourth member of the set, H1-69:L3-20, was crystallized with 2 Fabs in the asymmetric unit. RESULTS | |
| 67 71 Fabs structure_element The fourth member of the set, H1-69:L3-20, was crystallized with 2 Fabs in the asymmetric unit. RESULTS | |
| 20 23 CDR structure_element The conformation of CDR L1 in these 2 Fabs is slightly different, and both conformations fall somewhere between L1-12-1 and L1-12-2. RESULTS | |
| 24 26 L1 structure_element The conformation of CDR L1 in these 2 Fabs is slightly different, and both conformations fall somewhere between L1-12-1 and L1-12-2. RESULTS | |
| 38 42 Fabs structure_element The conformation of CDR L1 in these 2 Fabs is slightly different, and both conformations fall somewhere between L1-12-1 and L1-12-2. RESULTS | |
| 112 119 L1-12-1 mutant The conformation of CDR L1 in these 2 Fabs is slightly different, and both conformations fall somewhere between L1-12-1 and L1-12-2. RESULTS | |
| 124 131 L1-12-2 mutant The conformation of CDR L1 in these 2 Fabs is slightly different, and both conformations fall somewhere between L1-12-1 and L1-12-2. RESULTS | |
| 42 51 structure evidence This reflects the lack of accuracy in the structure due to low resolution of the X-ray data (3.3 Å). RESULTS | |
| 81 91 X-ray data evidence This reflects the lack of accuracy in the structure due to low resolution of the X-ray data (3.3 Å). RESULTS | |
| 0 3 CDR structure_element CDR L2 RESULTS | |
| 4 6 L2 structure_element CDR L2 RESULTS | |
| 4 17 superposition experimental_method The superposition of CDR L2 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 21 24 CDR structure_element The superposition of CDR L2 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 25 27 L2 structure_element The superposition of CDR L2 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 46 51 HC:LC complex_assembly The superposition of CDR L2 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 63 75 light chains structure_element The superposition of CDR L2 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 81 86 L1-39 mutant The superposition of CDR L2 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 92 97 L3-11 mutant The superposition of CDR L2 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 103 108 L3-20 mutant The superposition of CDR L2 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 117 121 L4-1 mutant The superposition of CDR L2 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 9 12 LCs structure_element All four LCs have CDR L2 of the same length and canonical structure, L2-8-1 (Table 2). RESULTS | |
| 18 21 CDR structure_element All four LCs have CDR L2 of the same length and canonical structure, L2-8-1 (Table 2). RESULTS | |
| 22 24 L2 structure_element All four LCs have CDR L2 of the same length and canonical structure, L2-8-1 (Table 2). RESULTS | |
| 69 75 L2-8-1 mutant All four LCs have CDR L2 of the same length and canonical structure, L2-8-1 (Table 2). RESULTS | |
| 4 7 CDR structure_element The CDR L2 conformations for each of the LCs paired with the 4 HCs are clustered more tightly than any of the other CDRs (rmsd values are in the range 0.09-0.16 Å), and all 4 sets have virtually the same conformation despite the sequence diversity of the loop. RESULTS | |
| 8 10 L2 structure_element The CDR L2 conformations for each of the LCs paired with the 4 HCs are clustered more tightly than any of the other CDRs (rmsd values are in the range 0.09-0.16 Å), and all 4 sets have virtually the same conformation despite the sequence diversity of the loop. RESULTS | |
| 41 44 LCs structure_element The CDR L2 conformations for each of the LCs paired with the 4 HCs are clustered more tightly than any of the other CDRs (rmsd values are in the range 0.09-0.16 Å), and all 4 sets have virtually the same conformation despite the sequence diversity of the loop. RESULTS | |
| 63 66 HCs structure_element The CDR L2 conformations for each of the LCs paired with the 4 HCs are clustered more tightly than any of the other CDRs (rmsd values are in the range 0.09-0.16 Å), and all 4 sets have virtually the same conformation despite the sequence diversity of the loop. RESULTS | |
| 116 120 CDRs structure_element The CDR L2 conformations for each of the LCs paired with the 4 HCs are clustered more tightly than any of the other CDRs (rmsd values are in the range 0.09-0.16 Å), and all 4 sets have virtually the same conformation despite the sequence diversity of the loop. RESULTS | |
| 122 126 rmsd evidence The CDR L2 conformations for each of the LCs paired with the 4 HCs are clustered more tightly than any of the other CDRs (rmsd values are in the range 0.09-0.16 Å), and all 4 sets have virtually the same conformation despite the sequence diversity of the loop. RESULTS | |
| 255 259 loop structure_element The CDR L2 conformations for each of the LCs paired with the 4 HCs are clustered more tightly than any of the other CDRs (rmsd values are in the range 0.09-0.16 Å), and all 4 sets have virtually the same conformation despite the sequence diversity of the loop. RESULTS | |
| 0 3 CDR structure_element CDR L3 RESULTS | |
| 4 6 L3 structure_element CDR L3 RESULTS | |
| 4 17 superposition experimental_method The superposition of CDR L3 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 21 24 CDR structure_element The superposition of CDR L3 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 25 27 L3 structure_element The superposition of CDR L3 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 46 51 HC:LC complex_assembly The superposition of CDR L3 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 63 75 light chains structure_element The superposition of CDR L3 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 81 86 L1-39 mutant The superposition of CDR L3 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 92 97 L3-11 mutant The superposition of CDR L3 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 103 108 L3-20 mutant The superposition of CDR L3 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 117 121 L4-1 mutant The superposition of CDR L3 backbones for all HC:LC pairs with light chains: (A) L1-39, (B) L3-11, (C) L3-20 and (D) L4-1. FIG | |
| 8 11 CDR structure_element As with CDR L2, all 4 LCs have CDR L3 of the same length and canonical structure, L3-9-cis7-1 (Table 2). RESULTS | |
| 12 14 L2 structure_element As with CDR L2, all 4 LCs have CDR L3 of the same length and canonical structure, L3-9-cis7-1 (Table 2). RESULTS | |
| 22 25 LCs structure_element As with CDR L2, all 4 LCs have CDR L3 of the same length and canonical structure, L3-9-cis7-1 (Table 2). RESULTS | |
| 31 34 CDR structure_element As with CDR L2, all 4 LCs have CDR L3 of the same length and canonical structure, L3-9-cis7-1 (Table 2). RESULTS | |
| 35 37 L3 structure_element As with CDR L2, all 4 LCs have CDR L3 of the same length and canonical structure, L3-9-cis7-1 (Table 2). RESULTS | |
| 71 80 structure evidence As with CDR L2, all 4 LCs have CDR L3 of the same length and canonical structure, L3-9-cis7-1 (Table 2). RESULTS | |
| 82 93 L3-9-cis7-1 mutant As with CDR L2, all 4 LCs have CDR L3 of the same length and canonical structure, L3-9-cis7-1 (Table 2). RESULTS | |
| 21 24 CDR structure_element The conformations of CDR L3 for L1-39, L3-11, and particularly for L320, are not as tightly clustered as those of L4-1 (Fig. 5). RESULTS | |
| 25 27 L3 structure_element The conformations of CDR L3 for L1-39, L3-11, and particularly for L320, are not as tightly clustered as those of L4-1 (Fig. 5). RESULTS | |
| 32 37 L1-39 mutant The conformations of CDR L3 for L1-39, L3-11, and particularly for L320, are not as tightly clustered as those of L4-1 (Fig. 5). RESULTS | |
| 39 44 L3-11 mutant The conformations of CDR L3 for L1-39, L3-11, and particularly for L320, are not as tightly clustered as those of L4-1 (Fig. 5). RESULTS | |
| 114 118 L4-1 mutant The conformations of CDR L3 for L1-39, L3-11, and particularly for L320, are not as tightly clustered as those of L4-1 (Fig. 5). RESULTS | |
| 82 87 90-92 residue_range The slight conformational variability occurs in the region of amino acid residues 90-92, which is in contact with CDR H3. RESULTS | |
| 114 117 CDR structure_element The slight conformational variability occurs in the region of amino acid residues 90-92, which is in contact with CDR H3. RESULTS | |
| 118 120 H3 structure_element The slight conformational variability occurs in the region of amino acid residues 90-92, which is in contact with CDR H3. RESULTS | |
| 0 3 CDR structure_element CDR H3 conformational diversity RESULTS | |
| 4 6 H3 structure_element CDR H3 conformational diversity RESULTS | |
| 29 33 Fabs structure_element As mentioned earlier, all 16 Fabs have the same CDR H3, for which the amino acid sequence is derived from the anti-CCL2 antibody CNTO 888. RESULTS | |
| 48 51 CDR structure_element As mentioned earlier, all 16 Fabs have the same CDR H3, for which the amino acid sequence is derived from the anti-CCL2 antibody CNTO 888. RESULTS | |
| 52 54 H3 structure_element As mentioned earlier, all 16 Fabs have the same CDR H3, for which the amino acid sequence is derived from the anti-CCL2 antibody CNTO 888. RESULTS | |
| 120 128 antibody protein_type As mentioned earlier, all 16 Fabs have the same CDR H3, for which the amino acid sequence is derived from the anti-CCL2 antibody CNTO 888. RESULTS | |
| 129 137 CNTO 888 chemical As mentioned earlier, all 16 Fabs have the same CDR H3, for which the amino acid sequence is derived from the anti-CCL2 antibody CNTO 888. RESULTS | |
| 4 8 loop structure_element The loop and the 2 β-strands of the CDR H3 in this ‘parent’ structure are stabilized by H-bonds between the carbonyl oxygen and peptide nitrogen atoms in the 2 strands. RESULTS | |
| 19 28 β-strands structure_element The loop and the 2 β-strands of the CDR H3 in this ‘parent’ structure are stabilized by H-bonds between the carbonyl oxygen and peptide nitrogen atoms in the 2 strands. RESULTS | |
| 36 39 CDR structure_element The loop and the 2 β-strands of the CDR H3 in this ‘parent’ structure are stabilized by H-bonds between the carbonyl oxygen and peptide nitrogen atoms in the 2 strands. RESULTS | |
| 40 42 H3 structure_element The loop and the 2 β-strands of the CDR H3 in this ‘parent’ structure are stabilized by H-bonds between the carbonyl oxygen and peptide nitrogen atoms in the 2 strands. RESULTS | |
| 60 69 structure evidence The loop and the 2 β-strands of the CDR H3 in this ‘parent’ structure are stabilized by H-bonds between the carbonyl oxygen and peptide nitrogen atoms in the 2 strands. RESULTS | |
| 88 95 H-bonds bond_interaction The loop and the 2 β-strands of the CDR H3 in this ‘parent’ structure are stabilized by H-bonds between the carbonyl oxygen and peptide nitrogen atoms in the 2 strands. RESULTS | |
| 32 35 CDR structure_element An interesting feature of these CDR H3 structures is the presence of a water molecule that interacts with the peptide nitrogens and carbonyl oxygens near the bridging loop connecting the 2 β-strands. RESULTS | |
| 36 38 H3 structure_element An interesting feature of these CDR H3 structures is the presence of a water molecule that interacts with the peptide nitrogens and carbonyl oxygens near the bridging loop connecting the 2 β-strands. RESULTS | |
| 39 49 structures evidence An interesting feature of these CDR H3 structures is the presence of a water molecule that interacts with the peptide nitrogens and carbonyl oxygens near the bridging loop connecting the 2 β-strands. RESULTS | |
| 71 76 water chemical An interesting feature of these CDR H3 structures is the presence of a water molecule that interacts with the peptide nitrogens and carbonyl oxygens near the bridging loop connecting the 2 β-strands. RESULTS | |
| 167 171 loop structure_element An interesting feature of these CDR H3 structures is the presence of a water molecule that interacts with the peptide nitrogens and carbonyl oxygens near the bridging loop connecting the 2 β-strands. RESULTS | |
| 189 198 β-strands structure_element An interesting feature of these CDR H3 structures is the presence of a water molecule that interacts with the peptide nitrogens and carbonyl oxygens near the bridging loop connecting the 2 β-strands. RESULTS | |
| 5 10 water chemical This water is present in both the bound (4DN4) and unbound (4DN3) forms of CNTO 888. RESULTS | |
| 34 39 bound protein_state This water is present in both the bound (4DN4) and unbound (4DN3) forms of CNTO 888. RESULTS | |
| 51 58 unbound protein_state This water is present in both the bound (4DN4) and unbound (4DN3) forms of CNTO 888. RESULTS | |
| 75 83 CNTO 888 chemical This water is present in both the bound (4DN4) and unbound (4DN3) forms of CNTO 888. RESULTS | |
| 4 15 stem region structure_element The stem region of CDR H3 in the parental Fab is in a ‘kinked’ conformation, in which the indole nitrogen of Trp103 forms a hydrogen bond with the carbonyl oxygen of Leu100b. RESULTS | |
| 19 22 CDR structure_element The stem region of CDR H3 in the parental Fab is in a ‘kinked’ conformation, in which the indole nitrogen of Trp103 forms a hydrogen bond with the carbonyl oxygen of Leu100b. RESULTS | |
| 23 25 H3 structure_element The stem region of CDR H3 in the parental Fab is in a ‘kinked’ conformation, in which the indole nitrogen of Trp103 forms a hydrogen bond with the carbonyl oxygen of Leu100b. RESULTS | |
| 42 45 Fab structure_element The stem region of CDR H3 in the parental Fab is in a ‘kinked’ conformation, in which the indole nitrogen of Trp103 forms a hydrogen bond with the carbonyl oxygen of Leu100b. RESULTS | |
| 55 61 kinked protein_state The stem region of CDR H3 in the parental Fab is in a ‘kinked’ conformation, in which the indole nitrogen of Trp103 forms a hydrogen bond with the carbonyl oxygen of Leu100b. RESULTS | |
| 109 115 Trp103 residue_name_number The stem region of CDR H3 in the parental Fab is in a ‘kinked’ conformation, in which the indole nitrogen of Trp103 forms a hydrogen bond with the carbonyl oxygen of Leu100b. RESULTS | |
| 124 137 hydrogen bond bond_interaction The stem region of CDR H3 in the parental Fab is in a ‘kinked’ conformation, in which the indole nitrogen of Trp103 forms a hydrogen bond with the carbonyl oxygen of Leu100b. RESULTS | |
| 166 173 Leu100b residue_name_number The stem region of CDR H3 in the parental Fab is in a ‘kinked’ conformation, in which the indole nitrogen of Trp103 forms a hydrogen bond with the carbonyl oxygen of Leu100b. RESULTS | |
| 22 28 Asp101 residue_name_number The carboxyl group of Asp101 forms a salt bridge with Arg94. RESULTS | |
| 37 48 salt bridge bond_interaction The carboxyl group of Asp101 forms a salt bridge with Arg94. RESULTS | |
| 54 59 Arg94 residue_name_number The carboxyl group of Asp101 forms a salt bridge with Arg94. RESULTS | |
| 34 47 superposition experimental_method Ribbon representations of (A) the superposition of all CDR H3s of the structures with complete backbone traces. (B) The CDR H3s rotated 90° about the y axis of the page. FIG | |
| 55 58 CDR structure_element Ribbon representations of (A) the superposition of all CDR H3s of the structures with complete backbone traces. (B) The CDR H3s rotated 90° about the y axis of the page. FIG | |
| 59 62 H3s structure_element Ribbon representations of (A) the superposition of all CDR H3s of the structures with complete backbone traces. (B) The CDR H3s rotated 90° about the y axis of the page. FIG | |
| 70 80 structures evidence Ribbon representations of (A) the superposition of all CDR H3s of the structures with complete backbone traces. (B) The CDR H3s rotated 90° about the y axis of the page. FIG | |
| 120 123 CDR structure_element Ribbon representations of (A) the superposition of all CDR H3s of the structures with complete backbone traces. (B) The CDR H3s rotated 90° about the y axis of the page. FIG | |
| 124 127 H3s structure_element Ribbon representations of (A) the superposition of all CDR H3s of the structures with complete backbone traces. (B) The CDR H3s rotated 90° about the y axis of the page. FIG | |
| 4 13 structure evidence The structure of each CDR H3 is represented with a different color. FIG | |
| 22 25 CDR structure_element The structure of each CDR H3 is represented with a different color. FIG | |
| 26 28 H3 structure_element The structure of each CDR H3 is represented with a different color. FIG | |
| 61 64 CDR structure_element Despite having the same amino acid sequence in all variants, CDR H3 has the highest degree of structural diversity and disorder of all of the CDRs in the experimental set. RESULTS | |
| 65 67 H3 structure_element Despite having the same amino acid sequence in all variants, CDR H3 has the highest degree of structural diversity and disorder of all of the CDRs in the experimental set. RESULTS | |
| 142 146 CDRs structure_element Despite having the same amino acid sequence in all variants, CDR H3 has the highest degree of structural diversity and disorder of all of the CDRs in the experimental set. RESULTS | |
| 16 19 Fab structure_element Three of the 21 Fab structures (including multiple copies in the asymmetric unit), H5-51:L3-11, H551:L3-20 and H3-23:L4-1 (one of the 2 Fabs), have missing (disordered) residues at the apex of the CDR loop. RESULTS | |
| 20 30 structures evidence Three of the 21 Fab structures (including multiple copies in the asymmetric unit), H5-51:L3-11, H551:L3-20 and H3-23:L4-1 (one of the 2 Fabs), have missing (disordered) residues at the apex of the CDR loop. RESULTS | |
| 83 94 H5-51:L3-11 complex_assembly Three of the 21 Fab structures (including multiple copies in the asymmetric unit), H5-51:L3-11, H551:L3-20 and H3-23:L4-1 (one of the 2 Fabs), have missing (disordered) residues at the apex of the CDR loop. RESULTS | |
| 96 106 H551:L3-20 complex_assembly Three of the 21 Fab structures (including multiple copies in the asymmetric unit), H5-51:L3-11, H551:L3-20 and H3-23:L4-1 (one of the 2 Fabs), have missing (disordered) residues at the apex of the CDR loop. RESULTS | |
| 111 121 H3-23:L4-1 complex_assembly Three of the 21 Fab structures (including multiple copies in the asymmetric unit), H5-51:L3-11, H551:L3-20 and H3-23:L4-1 (one of the 2 Fabs), have missing (disordered) residues at the apex of the CDR loop. RESULTS | |
| 136 140 Fabs structure_element Three of the 21 Fab structures (including multiple copies in the asymmetric unit), H5-51:L3-11, H551:L3-20 and H3-23:L4-1 (one of the 2 Fabs), have missing (disordered) residues at the apex of the CDR loop. RESULTS | |
| 148 155 missing protein_state Three of the 21 Fab structures (including multiple copies in the asymmetric unit), H5-51:L3-11, H551:L3-20 and H3-23:L4-1 (one of the 2 Fabs), have missing (disordered) residues at the apex of the CDR loop. RESULTS | |
| 157 167 disordered protein_state Three of the 21 Fab structures (including multiple copies in the asymmetric unit), H5-51:L3-11, H551:L3-20 and H3-23:L4-1 (one of the 2 Fabs), have missing (disordered) residues at the apex of the CDR loop. RESULTS | |
| 197 205 CDR loop structure_element Three of the 21 Fab structures (including multiple copies in the asymmetric unit), H5-51:L3-11, H551:L3-20 and H3-23:L4-1 (one of the 2 Fabs), have missing (disordered) residues at the apex of the CDR loop. RESULTS | |
| 20 24 Fabs structure_element Another four of the Fabs, H3-23:L1-39, H3-53:L1-39, H3-53:L3-11 and H3-53:L4-1 have missing side-chain atoms. RESULTS | |
| 26 37 H3-23:L1-39 complex_assembly Another four of the Fabs, H3-23:L1-39, H3-53:L1-39, H3-53:L3-11 and H3-53:L4-1 have missing side-chain atoms. RESULTS | |
| 39 50 H3-53:L1-39 complex_assembly Another four of the Fabs, H3-23:L1-39, H3-53:L1-39, H3-53:L3-11 and H3-53:L4-1 have missing side-chain atoms. RESULTS | |
| 52 63 H3-53:L3-11 complex_assembly Another four of the Fabs, H3-23:L1-39, H3-53:L1-39, H3-53:L3-11 and H3-53:L4-1 have missing side-chain atoms. RESULTS | |
| 68 78 H3-53:L4-1 complex_assembly Another four of the Fabs, H3-23:L1-39, H3-53:L1-39, H3-53:L3-11 and H3-53:L4-1 have missing side-chain atoms. RESULTS | |
| 18 21 CDR structure_element The variations in CDR H3 conformation are illustrated in Fig. 6 for the 18 Fab structures that have ordered backbone atoms. RESULTS | |
| 22 24 H3 structure_element The variations in CDR H3 conformation are illustrated in Fig. 6 for the 18 Fab structures that have ordered backbone atoms. RESULTS | |
| 75 78 Fab structure_element The variations in CDR H3 conformation are illustrated in Fig. 6 for the 18 Fab structures that have ordered backbone atoms. RESULTS | |
| 79 89 structures evidence The variations in CDR H3 conformation are illustrated in Fig. 6 for the 18 Fab structures that have ordered backbone atoms. RESULTS | |
| 40 46 kinked protein_state A comparison of representatives of the “kinked” and “extended” structures. FIG | |
| 53 61 extended protein_state A comparison of representatives of the “kinked” and “extended” structures. FIG | |
| 63 73 structures evidence A comparison of representatives of the “kinked” and “extended” structures. FIG | |
| 9 15 kinked protein_state (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 17 20 CDR structure_element (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 21 23 H3 structure_element (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 27 38 H1-69:L3-11 complex_assembly (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 120 127 Leu100b residue_name_number (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 134 140 Trp103 residue_name_number (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 146 151 Arg94 residue_name_number (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 159 165 Asp101 residue_name_number (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 175 180 Arg94 residue_name_number (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 189 195 Asp101 residue_name_number (A) The “kinked” CDR H3 of H1-69:L3-11 with purple carbon atoms and yellow dashed lines connecting the H-bond pairs for Leu100b O and Trp103 NE1, Arg94 NE and Asp101 OD1, and Arg94 NH2 and Asp101 OD2. FIG | |
| 9 17 extended protein_state (B) The “extended” CDR H3 of H1-69:L3-20 with green carbon atoms and yellow dashed lines connecting the H-bond pairs for Asp101 OD1 and OD2 and Trp103 NE1. FIG | |
| 19 22 CDR structure_element (B) The “extended” CDR H3 of H1-69:L3-20 with green carbon atoms and yellow dashed lines connecting the H-bond pairs for Asp101 OD1 and OD2 and Trp103 NE1. FIG | |
| 23 25 H3 structure_element (B) The “extended” CDR H3 of H1-69:L3-20 with green carbon atoms and yellow dashed lines connecting the H-bond pairs for Asp101 OD1 and OD2 and Trp103 NE1. FIG | |
| 29 40 H1-69:L3-20 complex_assembly (B) The “extended” CDR H3 of H1-69:L3-20 with green carbon atoms and yellow dashed lines connecting the H-bond pairs for Asp101 OD1 and OD2 and Trp103 NE1. FIG | |
| 121 127 Asp101 residue_name_number (B) The “extended” CDR H3 of H1-69:L3-20 with green carbon atoms and yellow dashed lines connecting the H-bond pairs for Asp101 OD1 and OD2 and Trp103 NE1. FIG | |
| 144 150 Trp103 residue_name_number (B) The “extended” CDR H3 of H1-69:L3-20 with green carbon atoms and yellow dashed lines connecting the H-bond pairs for Asp101 OD1 and OD2 and Trp103 NE1. FIG | |
| 16 19 Fab structure_element In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 20 30 structures evidence In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 32 43 H1-69:L1-39 complex_assembly In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 45 56 H1-69:L3-11 complex_assembly In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 60 64 Fabs structure_element In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 67 77 H1-69:L4-1 complex_assembly In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 79 90 H3-23:L3-11 complex_assembly In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 94 98 Fabs structure_element In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 101 112 H3-23:L3-20 complex_assembly In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 114 125 H3-53:L3-11 complex_assembly In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 127 138 H3-53:L3-20 complex_assembly In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 143 154 H5-51:L1-39 complex_assembly In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 160 164 CDRs structure_element In 10 of the 18 Fab structures, H1-69:L1-39, H1-69:L3-11 (2 Fabs), H1-69:L4-1, H3-23:L3-11 (2 Fabs), H3-23:L3-20, H3-53:L3-11, H3-53:L3-20 and H5-51:L1-39, the CDRs have similar conformations to that found in 4DN3. RESULTS | |
| 19 29 structures evidence The bases of these structures have the ‘kinked’ conformation with the H-bond between Trp103 and Leu100b. RESULTS | |
| 40 46 kinked protein_state The bases of these structures have the ‘kinked’ conformation with the H-bond between Trp103 and Leu100b. RESULTS | |
| 85 91 Trp103 residue_name_number The bases of these structures have the ‘kinked’ conformation with the H-bond between Trp103 and Leu100b. RESULTS | |
| 96 103 Leu100b residue_name_number The bases of these structures have the ‘kinked’ conformation with the H-bond between Trp103 and Leu100b. RESULTS | |
| 17 20 CDR structure_element A representative CDR H3 structure for H1-69:L1-39 illustrating this is shown in Fig. 7A. RESULTS | |
| 21 23 H3 structure_element A representative CDR H3 structure for H1-69:L1-39 illustrating this is shown in Fig. 7A. RESULTS | |
| 24 33 structure evidence A representative CDR H3 structure for H1-69:L1-39 illustrating this is shown in Fig. 7A. RESULTS | |
| 38 49 H1-69:L1-39 complex_assembly A representative CDR H3 structure for H1-69:L1-39 illustrating this is shown in Fig. 7A. RESULTS | |
| 64 69 Tyr99 residue_name_number The largest backbone conformational deviation for the set is at Tyr99, where the C=O is rotated by 90° relative to that observed in 4DN3. RESULTS | |
| 48 58 structures evidence Also, it is worth noting that only one of these structures, H1-69:L4-1, has the conserved water molecule in CDR H3 observed in the 4DN3 and 4DN4 structures. RESULTS | |
| 60 70 H1-69:L4-1 complex_assembly Also, it is worth noting that only one of these structures, H1-69:L4-1, has the conserved water molecule in CDR H3 observed in the 4DN3 and 4DN4 structures. RESULTS | |
| 80 89 conserved protein_state Also, it is worth noting that only one of these structures, H1-69:L4-1, has the conserved water molecule in CDR H3 observed in the 4DN3 and 4DN4 structures. RESULTS | |
| 90 95 water chemical Also, it is worth noting that only one of these structures, H1-69:L4-1, has the conserved water molecule in CDR H3 observed in the 4DN3 and 4DN4 structures. RESULTS | |
| 108 111 CDR structure_element Also, it is worth noting that only one of these structures, H1-69:L4-1, has the conserved water molecule in CDR H3 observed in the 4DN3 and 4DN4 structures. RESULTS | |
| 112 114 H3 structure_element Also, it is worth noting that only one of these structures, H1-69:L4-1, has the conserved water molecule in CDR H3 observed in the 4DN3 and 4DN4 structures. RESULTS | |
| 145 155 structures evidence Also, it is worth noting that only one of these structures, H1-69:L4-1, has the conserved water molecule in CDR H3 observed in the 4DN3 and 4DN4 structures. RESULTS | |
| 24 27 Fab structure_element In fact, it is the only Fab in the set that has a water molecule present at this site. RESULTS | |
| 50 55 water chemical In fact, it is the only Fab in the set that has a water molecule present at this site. RESULTS | |
| 4 7 CDR structure_element The CDR H3 for this structure is shown in Fig. S3. RESULTS | |
| 8 10 H3 structure_element The CDR H3 for this structure is shown in Fig. S3. RESULTS | |
| 20 29 structure evidence The CDR H3 for this structure is shown in Fig. S3. RESULTS | |
| 16 20 Fabs structure_element The remaining 8 Fabs can be grouped into 5 different conformational classes. RESULTS | |
| 13 17 Fabs structure_element Three of the Fabs, H3-23:L1-39, H3-23:L4-1 and H3-53:L1-39, have distinctive conformations. RESULTS | |
| 19 30 H3-23:L1-39 complex_assembly Three of the Fabs, H3-23:L1-39, H3-23:L4-1 and H3-53:L1-39, have distinctive conformations. RESULTS | |
| 32 42 H3-23:L4-1 complex_assembly Three of the Fabs, H3-23:L1-39, H3-23:L4-1 and H3-53:L1-39, have distinctive conformations. RESULTS | |
| 47 58 H3-53:L1-39 complex_assembly Three of the Fabs, H3-23:L1-39, H3-23:L4-1 and H3-53:L1-39, have distinctive conformations. RESULTS | |
| 4 16 stem regions structure_element The stem regions in these 3 cases are in the ‘kinked’ conformation consistent with that observed for 4DN3. RESULTS | |
| 46 52 kinked protein_state The stem regions in these 3 cases are in the ‘kinked’ conformation consistent with that observed for 4DN3. RESULTS | |
| 19 23 Fabs structure_element The five remaining Fabs, H5-51:L4-1 (2 copies), H1-69:L3-20 (2 copies) and H3-53:L4-1, have 3 different CDR H3 conformations (Fig. S4). RESULTS | |
| 25 35 H5-51:L4-1 complex_assembly The five remaining Fabs, H5-51:L4-1 (2 copies), H1-69:L3-20 (2 copies) and H3-53:L4-1, have 3 different CDR H3 conformations (Fig. S4). RESULTS | |
| 48 59 H1-69:L3-20 complex_assembly The five remaining Fabs, H5-51:L4-1 (2 copies), H1-69:L3-20 (2 copies) and H3-53:L4-1, have 3 different CDR H3 conformations (Fig. S4). RESULTS | |
| 75 85 H3-53:L4-1 complex_assembly The five remaining Fabs, H5-51:L4-1 (2 copies), H1-69:L3-20 (2 copies) and H3-53:L4-1, have 3 different CDR H3 conformations (Fig. S4). RESULTS | |
| 104 107 CDR structure_element The five remaining Fabs, H5-51:L4-1 (2 copies), H1-69:L3-20 (2 copies) and H3-53:L4-1, have 3 different CDR H3 conformations (Fig. S4). RESULTS | |
| 108 110 H3 structure_element The five remaining Fabs, H5-51:L4-1 (2 copies), H1-69:L3-20 (2 copies) and H3-53:L4-1, have 3 different CDR H3 conformations (Fig. S4). RESULTS | |
| 4 16 stem regions structure_element The stem regions of CDR H3 for the H5-51:L4-1 Fabs are in the ‘kinked’ conformation while, surprisingly, those of the H1-69:L3-20 pair and H3-53:L4-1 are in the ‘extended’ conformation (Fig. 7B). RESULTS | |
| 20 23 CDR structure_element The stem regions of CDR H3 for the H5-51:L4-1 Fabs are in the ‘kinked’ conformation while, surprisingly, those of the H1-69:L3-20 pair and H3-53:L4-1 are in the ‘extended’ conformation (Fig. 7B). RESULTS | |
| 24 26 H3 structure_element The stem regions of CDR H3 for the H5-51:L4-1 Fabs are in the ‘kinked’ conformation while, surprisingly, those of the H1-69:L3-20 pair and H3-53:L4-1 are in the ‘extended’ conformation (Fig. 7B). RESULTS | |
| 35 45 H5-51:L4-1 complex_assembly The stem regions of CDR H3 for the H5-51:L4-1 Fabs are in the ‘kinked’ conformation while, surprisingly, those of the H1-69:L3-20 pair and H3-53:L4-1 are in the ‘extended’ conformation (Fig. 7B). RESULTS | |
| 46 50 Fabs structure_element The stem regions of CDR H3 for the H5-51:L4-1 Fabs are in the ‘kinked’ conformation while, surprisingly, those of the H1-69:L3-20 pair and H3-53:L4-1 are in the ‘extended’ conformation (Fig. 7B). RESULTS | |
| 63 69 kinked protein_state The stem regions of CDR H3 for the H5-51:L4-1 Fabs are in the ‘kinked’ conformation while, surprisingly, those of the H1-69:L3-20 pair and H3-53:L4-1 are in the ‘extended’ conformation (Fig. 7B). RESULTS | |
| 118 129 H1-69:L3-20 complex_assembly The stem regions of CDR H3 for the H5-51:L4-1 Fabs are in the ‘kinked’ conformation while, surprisingly, those of the H1-69:L3-20 pair and H3-53:L4-1 are in the ‘extended’ conformation (Fig. 7B). RESULTS | |
| 139 149 H3-53:L4-1 complex_assembly The stem regions of CDR H3 for the H5-51:L4-1 Fabs are in the ‘kinked’ conformation while, surprisingly, those of the H1-69:L3-20 pair and H3-53:L4-1 are in the ‘extended’ conformation (Fig. 7B). RESULTS | |
| 162 170 extended protein_state The stem regions of CDR H3 for the H5-51:L4-1 Fabs are in the ‘kinked’ conformation while, surprisingly, those of the H1-69:L3-20 pair and H3-53:L4-1 are in the ‘extended’ conformation (Fig. 7B). RESULTS | |
| 0 5 VH:VL complex_assembly VH:VL domain packing RESULTS | |
| 4 6 VH structure_element The VH and VL domains have a β-sandwich structure (also often referred as a Greek key motif) and each is composed of a 4-stranded and a 5-stranded antiparallel β-sheets. RESULTS | |
| 11 13 VL structure_element The VH and VL domains have a β-sandwich structure (also often referred as a Greek key motif) and each is composed of a 4-stranded and a 5-stranded antiparallel β-sheets. RESULTS | |
| 29 49 β-sandwich structure structure_element The VH and VL domains have a β-sandwich structure (also often referred as a Greek key motif) and each is composed of a 4-stranded and a 5-stranded antiparallel β-sheets. RESULTS | |
| 76 91 Greek key motif structure_element The VH and VL domains have a β-sandwich structure (also often referred as a Greek key motif) and each is composed of a 4-stranded and a 5-stranded antiparallel β-sheets. RESULTS | |
| 119 168 4-stranded and a 5-stranded antiparallel β-sheets structure_element The VH and VL domains have a β-sandwich structure (also often referred as a Greek key motif) and each is composed of a 4-stranded and a 5-stranded antiparallel β-sheets. RESULTS | |
| 44 63 5-stranded β-sheets structure_element The two domains pack together such that the 5-stranded β-sheets, which have hydrophobic surfaces, interact with each other bringing the CDRs from both the VH and VL domains into close proximity. RESULTS | |
| 136 140 CDRs structure_element The two domains pack together such that the 5-stranded β-sheets, which have hydrophobic surfaces, interact with each other bringing the CDRs from both the VH and VL domains into close proximity. RESULTS | |
| 155 157 VH structure_element The two domains pack together such that the 5-stranded β-sheets, which have hydrophobic surfaces, interact with each other bringing the CDRs from both the VH and VL domains into close proximity. RESULTS | |
| 162 164 VL structure_element The two domains pack together such that the 5-stranded β-sheets, which have hydrophobic surfaces, interact with each other bringing the CDRs from both the VH and VL domains into close proximity. RESULTS | |
| 65 81 domain interface site The domain packing of the variants was assessed by computing the domain interface interactions, the VH:VL tilt angles, the buried surface area and surface complementarity. RESULTS | |
| 100 105 VH:VL complex_assembly The domain packing of the variants was assessed by computing the domain interface interactions, the VH:VL tilt angles, the buried surface area and surface complementarity. RESULTS | |
| 106 117 tilt angles evidence The domain packing of the variants was assessed by computing the domain interface interactions, the VH:VL tilt angles, the buried surface area and surface complementarity. RESULTS | |
| 0 15 VH:VL interface site VH:VL interface amino acid residue interactions RESULTS | |
| 4 13 conserved protein_state The conserved VH:VL interactions as viewed along the VH/VL axis. FIG | |
| 14 19 VH:VL complex_assembly The conserved VH:VL interactions as viewed along the VH/VL axis. FIG | |
| 53 55 VH structure_element The conserved VH:VL interactions as viewed along the VH/VL axis. FIG | |
| 56 58 VL structure_element The conserved VH:VL interactions as viewed along the VH/VL axis. FIG | |
| 4 6 VH structure_element The VH residues are in blue, the VL residues are in orange. FIG | |
| 33 35 VL structure_element The VH residues are in blue, the VL residues are in orange. FIG | |
| 4 19 VH:VL interface site The VH:VL interface is pseudosymmetric, and involves 2 stretches of the polypeptide chain from each domain, namely CDR3 and the framework region between CDRs 1 and 2. RESULTS | |
| 23 38 pseudosymmetric protein_state The VH:VL interface is pseudosymmetric, and involves 2 stretches of the polypeptide chain from each domain, namely CDR3 and the framework region between CDRs 1 and 2. RESULTS | |
| 115 119 CDR3 structure_element The VH:VL interface is pseudosymmetric, and involves 2 stretches of the polypeptide chain from each domain, namely CDR3 and the framework region between CDRs 1 and 2. RESULTS | |
| 128 144 framework region structure_element The VH:VL interface is pseudosymmetric, and involves 2 stretches of the polypeptide chain from each domain, namely CDR3 and the framework region between CDRs 1 and 2. RESULTS | |
| 153 165 CDRs 1 and 2 structure_element The VH:VL interface is pseudosymmetric, and involves 2 stretches of the polypeptide chain from each domain, namely CDR3 and the framework region between CDRs 1 and 2. RESULTS | |
| 21 44 antiparallel β-hairpins structure_element These stretches form antiparallel β-hairpins within the internal 5-stranded β-sheet. RESULTS | |
| 65 83 5-stranded β-sheet structure_element These stretches form antiparallel β-hairpins within the internal 5-stranded β-sheet. RESULTS | |
| 110 114 Fabs structure_element There are a few principal inter-domain interactions that are conserved not only in the experimental set of 16 Fabs, but in all human antibodies. RESULTS | |
| 127 132 human species There are a few principal inter-domain interactions that are conserved not only in the experimental set of 16 Fabs, but in all human antibodies. RESULTS | |
| 133 143 antibodies protein_type There are a few principal inter-domain interactions that are conserved not only in the experimental set of 16 Fabs, but in all human antibodies. RESULTS | |
| 29 42 hydrogen bond bond_interaction They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 51 52 L structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 53 58 Gln38 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 63 64 H structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 65 70 Gln39 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 75 76 H structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 77 82 Leu45 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 88 106 hydrophobic pocket site They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 115 116 L structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 117 122 Phe98 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 124 125 L structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 126 131 Tyr87 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 136 137 L structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 138 143 Pro44 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 148 149 L structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 150 155 Pro44 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 172 173 H structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 174 180 Trp103 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 189 190 L structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 191 196 Ala43 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 218 219 H structure_element They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 220 225 Tyr91 residue_name_number They include: 1) a bidentate hydrogen bond between L-Gln38 and H-Gln39; 2) H-Leu45 in a hydrophobic pocket between L-Phe98, L-Tyr87 and L-Pro44; 3) L-Pro44 stacked against H-Trp103; and 4) L-Ala43 opposite the face of H-Tyr91 (Fig. 8). RESULTS | |
| 22 23 L structure_element With the exception of L-Ala43, all other residues are conserved in human germlines. RESULTS | |
| 24 29 Ala43 residue_name_number With the exception of L-Ala43, all other residues are conserved in human germlines. RESULTS | |
| 67 72 human species With the exception of L-Ala43, all other residues are conserved in human germlines. RESULTS | |
| 9 11 43 residue_number Position 43 may be alternatively occupied by Ser, Val or Pro (as in L4-1), but the hydrophobic interaction with H-Tyr91 is preserved. RESULTS | |
| 45 48 Ser residue_name Position 43 may be alternatively occupied by Ser, Val or Pro (as in L4-1), but the hydrophobic interaction with H-Tyr91 is preserved. RESULTS | |
| 50 53 Val residue_name Position 43 may be alternatively occupied by Ser, Val or Pro (as in L4-1), but the hydrophobic interaction with H-Tyr91 is preserved. RESULTS | |
| 57 60 Pro residue_name Position 43 may be alternatively occupied by Ser, Val or Pro (as in L4-1), but the hydrophobic interaction with H-Tyr91 is preserved. RESULTS | |
| 68 72 L4-1 mutant Position 43 may be alternatively occupied by Ser, Val or Pro (as in L4-1), but the hydrophobic interaction with H-Tyr91 is preserved. RESULTS | |
| 83 106 hydrophobic interaction bond_interaction Position 43 may be alternatively occupied by Ser, Val or Pro (as in L4-1), but the hydrophobic interaction with H-Tyr91 is preserved. RESULTS | |
| 112 113 H structure_element Position 43 may be alternatively occupied by Ser, Val or Pro (as in L4-1), but the hydrophobic interaction with H-Tyr91 is preserved. RESULTS | |
| 114 119 Tyr91 residue_name_number Position 43 may be alternatively occupied by Ser, Val or Pro (as in L4-1), but the hydrophobic interaction with H-Tyr91 is preserved. RESULTS | |
| 56 61 VH:VL complex_assembly These core interactions provide enough stability to the VH:VL dimer so that additional VH-VL contacts can tolerate amino acid sequence variations in CDRs H3 and L3 that form part of the VH:VL interface. RESULTS | |
| 62 67 dimer oligomeric_state These core interactions provide enough stability to the VH:VL dimer so that additional VH-VL contacts can tolerate amino acid sequence variations in CDRs H3 and L3 that form part of the VH:VL interface. RESULTS | |
| 87 101 VH-VL contacts site These core interactions provide enough stability to the VH:VL dimer so that additional VH-VL contacts can tolerate amino acid sequence variations in CDRs H3 and L3 that form part of the VH:VL interface. RESULTS | |
| 149 153 CDRs structure_element These core interactions provide enough stability to the VH:VL dimer so that additional VH-VL contacts can tolerate amino acid sequence variations in CDRs H3 and L3 that form part of the VH:VL interface. RESULTS | |
| 154 156 H3 structure_element These core interactions provide enough stability to the VH:VL dimer so that additional VH-VL contacts can tolerate amino acid sequence variations in CDRs H3 and L3 that form part of the VH:VL interface. RESULTS | |
| 161 163 L3 structure_element These core interactions provide enough stability to the VH:VL dimer so that additional VH-VL contacts can tolerate amino acid sequence variations in CDRs H3 and L3 that form part of the VH:VL interface. RESULTS | |
| 186 201 VH:VL interface site These core interactions provide enough stability to the VH:VL dimer so that additional VH-VL contacts can tolerate amino acid sequence variations in CDRs H3 and L3 that form part of the VH:VL interface. RESULTS | |
| 16 27 20 residues residue_range In total, about 20 residues are involved in the VH:VL interactions on each side (Fig. S5). RESULTS | |
| 48 53 VH:VL complex_assembly In total, about 20 residues are involved in the VH:VL interactions on each side (Fig. S5). RESULTS | |
| 24 41 framework regions structure_element Half of them are in the framework regions and those residues (except residue 61 in HC, which is actually in CDR2 in Kabat's definition) are conserved in the set of 16 Fabs. RESULTS | |
| 77 79 61 residue_number Half of them are in the framework regions and those residues (except residue 61 in HC, which is actually in CDR2 in Kabat's definition) are conserved in the set of 16 Fabs. RESULTS | |
| 83 85 HC structure_element Half of them are in the framework regions and those residues (except residue 61 in HC, which is actually in CDR2 in Kabat's definition) are conserved in the set of 16 Fabs. RESULTS | |
| 108 112 CDR2 structure_element Half of them are in the framework regions and those residues (except residue 61 in HC, which is actually in CDR2 in Kabat's definition) are conserved in the set of 16 Fabs. RESULTS | |
| 167 171 Fabs structure_element Half of them are in the framework regions and those residues (except residue 61 in HC, which is actually in CDR2 in Kabat's definition) are conserved in the set of 16 Fabs. RESULTS | |
| 25 26 H structure_element One notable exception is H-Trp47, which exhibits 2 conformations of the indole ring. RESULTS | |
| 27 32 Trp47 residue_name_number One notable exception is H-Trp47, which exhibits 2 conformations of the indole ring. RESULTS | |
| 15 25 structures evidence In most of the structures, it has the χ2 angle of ∼80°, while the ring is flipped over (χ2 = −100°) in H5-51:L3:11 and H5-51:L3-20. RESULTS | |
| 38 40 χ2 evidence In most of the structures, it has the χ2 angle of ∼80°, while the ring is flipped over (χ2 = −100°) in H5-51:L3:11 and H5-51:L3-20. RESULTS | |
| 88 90 χ2 evidence In most of the structures, it has the χ2 angle of ∼80°, while the ring is flipped over (χ2 = −100°) in H5-51:L3:11 and H5-51:L3-20. RESULTS | |
| 103 114 H5-51:L3:11 complex_assembly In most of the structures, it has the χ2 angle of ∼80°, while the ring is flipped over (χ2 = −100°) in H5-51:L3:11 and H5-51:L3-20. RESULTS | |
| 119 130 H5-51:L3-20 complex_assembly In most of the structures, it has the χ2 angle of ∼80°, while the ring is flipped over (χ2 = −100°) in H5-51:L3:11 and H5-51:L3-20. RESULTS | |
| 36 46 structures evidence Interestingly, these are the only 2 structures with residues missing in CDR H3 because of disorder, although both structures are determined at high resolution and the rest of the structure is well defined. RESULTS | |
| 61 68 missing protein_state Interestingly, these are the only 2 structures with residues missing in CDR H3 because of disorder, although both structures are determined at high resolution and the rest of the structure is well defined. RESULTS | |
| 72 75 CDR structure_element Interestingly, these are the only 2 structures with residues missing in CDR H3 because of disorder, although both structures are determined at high resolution and the rest of the structure is well defined. RESULTS | |
| 76 78 H3 structure_element Interestingly, these are the only 2 structures with residues missing in CDR H3 because of disorder, although both structures are determined at high resolution and the rest of the structure is well defined. RESULTS | |
| 114 124 structures evidence Interestingly, these are the only 2 structures with residues missing in CDR H3 because of disorder, although both structures are determined at high resolution and the rest of the structure is well defined. RESULTS | |
| 179 188 structure evidence Interestingly, these are the only 2 structures with residues missing in CDR H3 because of disorder, although both structures are determined at high resolution and the rest of the structure is well defined. RESULTS | |
| 30 33 CDR structure_element Apparently, residues flanking CDR H3 in the 2 VH:VL pairings are inconsistent with any stable conformation of CDR H3, which translates into a less restricted conformational space for some of them, including H-Trp47. RESULTS | |
| 34 36 H3 structure_element Apparently, residues flanking CDR H3 in the 2 VH:VL pairings are inconsistent with any stable conformation of CDR H3, which translates into a less restricted conformational space for some of them, including H-Trp47. RESULTS | |
| 46 51 VH:VL complex_assembly Apparently, residues flanking CDR H3 in the 2 VH:VL pairings are inconsistent with any stable conformation of CDR H3, which translates into a less restricted conformational space for some of them, including H-Trp47. RESULTS | |
| 87 93 stable protein_state Apparently, residues flanking CDR H3 in the 2 VH:VL pairings are inconsistent with any stable conformation of CDR H3, which translates into a less restricted conformational space for some of them, including H-Trp47. RESULTS | |
| 110 113 CDR structure_element Apparently, residues flanking CDR H3 in the 2 VH:VL pairings are inconsistent with any stable conformation of CDR H3, which translates into a less restricted conformational space for some of them, including H-Trp47. RESULTS | |
| 114 116 H3 structure_element Apparently, residues flanking CDR H3 in the 2 VH:VL pairings are inconsistent with any stable conformation of CDR H3, which translates into a less restricted conformational space for some of them, including H-Trp47. RESULTS | |
| 207 208 H structure_element Apparently, residues flanking CDR H3 in the 2 VH:VL pairings are inconsistent with any stable conformation of CDR H3, which translates into a less restricted conformational space for some of them, including H-Trp47. RESULTS | |
| 209 214 Trp47 residue_name_number Apparently, residues flanking CDR H3 in the 2 VH:VL pairings are inconsistent with any stable conformation of CDR H3, which translates into a less restricted conformational space for some of them, including H-Trp47. RESULTS | |
| 0 5 VH:VL complex_assembly VH:VL tilt angles RESULTS | |
| 6 17 tilt angles evidence VH:VL tilt angles RESULTS | |
| 28 30 VH structure_element The relative orientation of VH and VL has been measured in a number of different ways. RESULTS | |
| 35 37 VL structure_element The relative orientation of VH and VL has been measured in a number of different ways. RESULTS | |
| 24 32 ABangles experimental_method The first approach uses ABangles, the results of which are shown in Table S2. RESULTS | |
| 9 12 LCs structure_element The four LCs all are classified as Type A because they have a proline at position 44, and the results for each orientation parameter are within the range of values of this type reported by Dunbar and co-workers. RESULTS | |
| 62 69 proline residue_name The four LCs all are classified as Type A because they have a proline at position 44, and the results for each orientation parameter are within the range of values of this type reported by Dunbar and co-workers. RESULTS | |
| 82 84 44 residue_number The four LCs all are classified as Type A because they have a proline at position 44, and the results for each orientation parameter are within the range of values of this type reported by Dunbar and co-workers. RESULTS | |
| 111 132 orientation parameter evidence The four LCs all are classified as Type A because they have a proline at position 44, and the results for each orientation parameter are within the range of values of this type reported by Dunbar and co-workers. RESULTS | |
| 48 52 Fabs structure_element In fact, the parameter values for the set of 16 Fabs are in the middle of the distribution observed for 351 non-redundant antibody structures determined at 3.0 Å resolution or better. RESULTS | |
| 122 130 antibody protein_type In fact, the parameter values for the set of 16 Fabs are in the middle of the distribution observed for 351 non-redundant antibody structures determined at 3.0 Å resolution or better. RESULTS | |
| 131 141 structures evidence In fact, the parameter values for the set of 16 Fabs are in the middle of the distribution observed for 351 non-redundant antibody structures determined at 3.0 Å resolution or better. RESULTS | |
| 22 25 HC1 structure_element The only exception is HC1, which is shifted toward smaller angles with the mean value of 70.8° as compared to the distribution centered at 72° for the entire PDB. RESULTS | |
| 41 44 CDR structure_element This probably reflects the invariance of CDR H3 in the current set as opposed to the CDR H3 diversity in the PDB. RESULTS | |
| 45 47 H3 structure_element This probably reflects the invariance of CDR H3 in the current set as opposed to the CDR H3 diversity in the PDB. RESULTS | |
| 85 88 CDR structure_element This probably reflects the invariance of CDR H3 in the current set as opposed to the CDR H3 diversity in the PDB. RESULTS | |
| 89 91 H3 structure_element This probably reflects the invariance of CDR H3 in the current set as opposed to the CDR H3 diversity in the PDB. RESULTS | |
| 39 50 tilt angles evidence The second approach used for comparing tilt angles involved computing the difference in the tilt angles between all pairs of structures. RESULTS | |
| 74 84 difference evidence The second approach used for comparing tilt angles involved computing the difference in the tilt angles between all pairs of structures. RESULTS | |
| 92 103 tilt angles evidence The second approach used for comparing tilt angles involved computing the difference in the tilt angles between all pairs of structures. RESULTS | |
| 125 135 structures evidence The second approach used for comparing tilt angles involved computing the difference in the tilt angles between all pairs of structures. RESULTS | |
| 4 14 structures evidence For structures with 2 copies of the Fab in the asymmetric unit, only one structure was used. RESULTS | |
| 36 39 Fab structure_element For structures with 2 copies of the Fab in the asymmetric unit, only one structure was used. RESULTS | |
| 73 82 structure evidence For structures with 2 copies of the Fab in the asymmetric unit, only one structure was used. RESULTS | |
| 36 40 Fabs structure_element The differences between independent Fabs in the same structure are 4.9° for H1-69:L3-20, 1.6° for H1-69:L3-11, 1.4° for H3-23:L4-1, 3.3° for H3-23:L3-11, and 2.5° for H5-51:L4-1. RESULTS | |
| 53 62 structure evidence The differences between independent Fabs in the same structure are 4.9° for H1-69:L3-20, 1.6° for H1-69:L3-11, 1.4° for H3-23:L4-1, 3.3° for H3-23:L3-11, and 2.5° for H5-51:L4-1. RESULTS | |
| 76 87 H1-69:L3-20 complex_assembly The differences between independent Fabs in the same structure are 4.9° for H1-69:L3-20, 1.6° for H1-69:L3-11, 1.4° for H3-23:L4-1, 3.3° for H3-23:L3-11, and 2.5° for H5-51:L4-1. RESULTS | |
| 98 109 H1-69:L3-11 complex_assembly The differences between independent Fabs in the same structure are 4.9° for H1-69:L3-20, 1.6° for H1-69:L3-11, 1.4° for H3-23:L4-1, 3.3° for H3-23:L3-11, and 2.5° for H5-51:L4-1. RESULTS | |
| 120 130 H3-23:L4-1 complex_assembly The differences between independent Fabs in the same structure are 4.9° for H1-69:L3-20, 1.6° for H1-69:L3-11, 1.4° for H3-23:L4-1, 3.3° for H3-23:L3-11, and 2.5° for H5-51:L4-1. RESULTS | |
| 141 152 H3-23:L3-11 complex_assembly The differences between independent Fabs in the same structure are 4.9° for H1-69:L3-20, 1.6° for H1-69:L3-11, 1.4° for H3-23:L4-1, 3.3° for H3-23:L3-11, and 2.5° for H5-51:L4-1. RESULTS | |
| 167 177 H5-51:L4-1 complex_assembly The differences between independent Fabs in the same structure are 4.9° for H1-69:L3-20, 1.6° for H1-69:L3-11, 1.4° for H3-23:L4-1, 3.3° for H3-23:L3-11, and 2.5° for H5-51:L4-1. RESULTS | |
| 22 33 H1-69:L3-20 complex_assembly With the exception of H1-69:L3-20, the angles are within the range of 2-3° as are observed in the identical structures in the PDB. RESULTS | |
| 108 118 structures evidence With the exception of H1-69:L3-20, the angles are within the range of 2-3° as are observed in the identical structures in the PDB. RESULTS | |
| 3 14 H1-69:L3-20 complex_assembly In H1-69:L3-20, one of the Fabs is substantially disordered so that part of CDR H2 (the outer β-strand, residues 55-60) is completely missing. RESULTS | |
| 27 31 Fabs structure_element In H1-69:L3-20, one of the Fabs is substantially disordered so that part of CDR H2 (the outer β-strand, residues 55-60) is completely missing. RESULTS | |
| 49 59 disordered protein_state In H1-69:L3-20, one of the Fabs is substantially disordered so that part of CDR H2 (the outer β-strand, residues 55-60) is completely missing. RESULTS | |
| 76 79 CDR structure_element In H1-69:L3-20, one of the Fabs is substantially disordered so that part of CDR H2 (the outer β-strand, residues 55-60) is completely missing. RESULTS | |
| 80 82 H2 structure_element In H1-69:L3-20, one of the Fabs is substantially disordered so that part of CDR H2 (the outer β-strand, residues 55-60) is completely missing. RESULTS | |
| 94 102 β-strand structure_element In H1-69:L3-20, one of the Fabs is substantially disordered so that part of CDR H2 (the outer β-strand, residues 55-60) is completely missing. RESULTS | |
| 113 118 55-60 residue_range In H1-69:L3-20, one of the Fabs is substantially disordered so that part of CDR H2 (the outer β-strand, residues 55-60) is completely missing. RESULTS | |
| 58 60 VH structure_element This kind of disorder may compromise the integrity of the VH domain and its interaction with the VL. RESULTS | |
| 97 99 VL structure_element This kind of disorder may compromise the integrity of the VH domain and its interaction with the VL. RESULTS | |
| 13 16 Fab structure_element Indeed, this Fab has the largest twist angle HC2 within the experimental set that exceeds the mean value by 2.5 standard deviations (Table S2). RESULTS | |
| 33 44 twist angle evidence Indeed, this Fab has the largest twist angle HC2 within the experimental set that exceeds the mean value by 2.5 standard deviations (Table S2). RESULTS | |
| 45 48 HC2 structure_element Indeed, this Fab has the largest twist angle HC2 within the experimental set that exceeds the mean value by 2.5 standard deviations (Table S2). RESULTS | |
| 79 92 superposition experimental_method An illustration of the difference in tilt angle for 2 pairs of variants by the superposition of the VH domains of (A) H1-69:L3-20 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 10.5°) and (B) H1-69:L4-1 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 1.6°). FIG | |
| 100 102 VH structure_element An illustration of the difference in tilt angle for 2 pairs of variants by the superposition of the VH domains of (A) H1-69:L3-20 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 10.5°) and (B) H1-69:L4-1 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 1.6°). FIG | |
| 118 129 H1-69:L3-20 complex_assembly An illustration of the difference in tilt angle for 2 pairs of variants by the superposition of the VH domains of (A) H1-69:L3-20 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 10.5°) and (B) H1-69:L4-1 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 1.6°). FIG | |
| 141 152 H5-51:L1-39 complex_assembly An illustration of the difference in tilt angle for 2 pairs of variants by the superposition of the VH domains of (A) H1-69:L3-20 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 10.5°) and (B) H1-69:L4-1 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 1.6°). FIG | |
| 158 160 VL structure_element An illustration of the difference in tilt angle for 2 pairs of variants by the superposition of the VH domains of (A) H1-69:L3-20 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 10.5°) and (B) H1-69:L4-1 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 1.6°). FIG | |
| 219 229 H1-69:L4-1 complex_assembly An illustration of the difference in tilt angle for 2 pairs of variants by the superposition of the VH domains of (A) H1-69:L3-20 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 10.5°) and (B) H1-69:L4-1 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 1.6°). FIG | |
| 241 252 H5-51:L1-39 complex_assembly An illustration of the difference in tilt angle for 2 pairs of variants by the superposition of the VH domains of (A) H1-69:L3-20 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 10.5°) and (B) H1-69:L4-1 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 1.6°). FIG | |
| 258 260 VL structure_element An illustration of the difference in tilt angle for 2 pairs of variants by the superposition of the VH domains of (A) H1-69:L3-20 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 10.5°) and (B) H1-69:L4-1 on that of H5-51:L1-39 (the VL domain is off by a rigid-body roatation of 1.6°). FIG | |
| 15 20 VH:VL complex_assembly Differences in VH:VL tilt angles. TABLE | |
| 21 32 tilt angles evidence Differences in VH:VL tilt angles. TABLE | |
| 4 15 differences evidence The differences in the tilt angle are shown for all pairs of V regions in Table 3. RESULTS | |
| 23 33 tilt angle evidence The differences in the tilt angle are shown for all pairs of V regions in Table 3. RESULTS | |
| 61 70 V regions structure_element The differences in the tilt angle are shown for all pairs of V regions in Table 3. RESULTS | |
| 32 42 tilt angle evidence The smallest differences in the tilt angle are between the Fabs in isomorphous crystal forms. RESULTS | |
| 59 63 Fabs structure_element The smallest differences in the tilt angle are between the Fabs in isomorphous crystal forms. RESULTS | |
| 79 92 crystal forms evidence The smallest differences in the tilt angle are between the Fabs in isomorphous crystal forms. RESULTS | |
| 30 40 tilt angle evidence The largest deviations in the tilt angle, up to 11.0°, are found for 2 structures, H1-69:L3-20 and H3-23:L3-20, that stand out from the other Fabs. RESULTS | |
| 71 81 structures evidence The largest deviations in the tilt angle, up to 11.0°, are found for 2 structures, H1-69:L3-20 and H3-23:L3-20, that stand out from the other Fabs. RESULTS | |
| 83 94 H1-69:L3-20 complex_assembly The largest deviations in the tilt angle, up to 11.0°, are found for 2 structures, H1-69:L3-20 and H3-23:L3-20, that stand out from the other Fabs. RESULTS | |
| 99 110 H3-23:L3-20 complex_assembly The largest deviations in the tilt angle, up to 11.0°, are found for 2 structures, H1-69:L3-20 and H3-23:L3-20, that stand out from the other Fabs. RESULTS | |
| 142 146 Fabs structure_element The largest deviations in the tilt angle, up to 11.0°, are found for 2 structures, H1-69:L3-20 and H3-23:L3-20, that stand out from the other Fabs. RESULTS | |
| 13 23 structures evidence One of the 2 structures, H1-69:L3-20, has its CDR H3 in the ‘extended’ conformation; the other structure has it in the ‘kinked’ conformation. RESULTS | |
| 25 36 H1-69:L3-20 complex_assembly One of the 2 structures, H1-69:L3-20, has its CDR H3 in the ‘extended’ conformation; the other structure has it in the ‘kinked’ conformation. RESULTS | |
| 46 49 CDR structure_element One of the 2 structures, H1-69:L3-20, has its CDR H3 in the ‘extended’ conformation; the other structure has it in the ‘kinked’ conformation. RESULTS | |
| 50 52 H3 structure_element One of the 2 structures, H1-69:L3-20, has its CDR H3 in the ‘extended’ conformation; the other structure has it in the ‘kinked’ conformation. RESULTS | |
| 61 69 extended protein_state One of the 2 structures, H1-69:L3-20, has its CDR H3 in the ‘extended’ conformation; the other structure has it in the ‘kinked’ conformation. RESULTS | |
| 120 126 kinked protein_state One of the 2 structures, H1-69:L3-20, has its CDR H3 in the ‘extended’ conformation; the other structure has it in the ‘kinked’ conformation. RESULTS | |
| 76 87 tilt angles evidence Two examples illustrating large (10.5°) and small (1.6°) differences in the tilt angles are shown in Fig. 9. RESULTS | |
| 0 5 VH:VL complex_assembly VH:VL buried surface area and complementarity RESULTS | |
| 0 5 VH:VL complex_assembly VH:VL surface areas and surface complementarity. TABLE | |
| 25 28 CDR structure_element Some side chain atoms in CDR H3 are missing. TABLE | |
| 29 31 H3 structure_element Some side chain atoms in CDR H3 are missing. TABLE | |
| 12 15 CDR structure_element Residues in CDR H3 are missing: YGE in H5-51:L3-11, GIY in H5-51:L3-20. TABLE | |
| 16 18 H3 structure_element Residues in CDR H3 are missing: YGE in H5-51:L3-11, GIY in H5-51:L3-20. TABLE | |
| 32 35 YGE structure_element Residues in CDR H3 are missing: YGE in H5-51:L3-11, GIY in H5-51:L3-20. TABLE | |
| 39 50 H5-51:L3-11 complex_assembly Residues in CDR H3 are missing: YGE in H5-51:L3-11, GIY in H5-51:L3-20. TABLE | |
| 52 55 GIY structure_element Residues in CDR H3 are missing: YGE in H5-51:L3-11, GIY in H5-51:L3-20. TABLE | |
| 59 70 H5-51:L3-20 complex_assembly Residues in CDR H3 are missing: YGE in H5-51:L3-11, GIY in H5-51:L3-20. TABLE | |
| 19 23 PISA experimental_method The results of the PISA contact surface calculation and surface complementarity calculation are shown in Table 4. RESULTS | |
| 24 51 contact surface calculation experimental_method The results of the PISA contact surface calculation and surface complementarity calculation are shown in Table 4. RESULTS | |
| 56 91 surface complementarity calculation experimental_method The results of the PISA contact surface calculation and surface complementarity calculation are shown in Table 4. RESULTS | |
| 4 13 interface site The interface areas are calculated as the average of the VH and VL contact surfaces. RESULTS | |
| 57 83 VH and VL contact surfaces site The interface areas are calculated as the average of the VH and VL contact surfaces. RESULTS | |
| 14 24 structures evidence Six of the 16 structures have CDR H3 side chains or complete residues missing, and therefore their interfaces are much smaller than in the other 10 structures with complete CDRs (the results are provided for all Fabs for completeness). RESULTS | |
| 30 33 CDR structure_element Six of the 16 structures have CDR H3 side chains or complete residues missing, and therefore their interfaces are much smaller than in the other 10 structures with complete CDRs (the results are provided for all Fabs for completeness). RESULTS | |
| 34 36 H3 structure_element Six of the 16 structures have CDR H3 side chains or complete residues missing, and therefore their interfaces are much smaller than in the other 10 structures with complete CDRs (the results are provided for all Fabs for completeness). RESULTS | |
| 70 77 missing protein_state Six of the 16 structures have CDR H3 side chains or complete residues missing, and therefore their interfaces are much smaller than in the other 10 structures with complete CDRs (the results are provided for all Fabs for completeness). RESULTS | |
| 99 109 interfaces site Six of the 16 structures have CDR H3 side chains or complete residues missing, and therefore their interfaces are much smaller than in the other 10 structures with complete CDRs (the results are provided for all Fabs for completeness). RESULTS | |
| 148 158 structures evidence Six of the 16 structures have CDR H3 side chains or complete residues missing, and therefore their interfaces are much smaller than in the other 10 structures with complete CDRs (the results are provided for all Fabs for completeness). RESULTS | |
| 164 172 complete protein_state Six of the 16 structures have CDR H3 side chains or complete residues missing, and therefore their interfaces are much smaller than in the other 10 structures with complete CDRs (the results are provided for all Fabs for completeness). RESULTS | |
| 173 177 CDRs structure_element Six of the 16 structures have CDR H3 side chains or complete residues missing, and therefore their interfaces are much smaller than in the other 10 structures with complete CDRs (the results are provided for all Fabs for completeness). RESULTS | |
| 212 216 Fabs structure_element Six of the 16 structures have CDR H3 side chains or complete residues missing, and therefore their interfaces are much smaller than in the other 10 structures with complete CDRs (the results are provided for all Fabs for completeness). RESULTS | |
| 10 18 complete protein_state Among the complete structures, the interface areas range from 684 to 836 Å2. RESULTS | |
| 19 29 structures evidence Among the complete structures, the interface areas range from 684 to 836 Å2. RESULTS | |
| 35 44 interface site Among the complete structures, the interface areas range from 684 to 836 Å2. RESULTS | |
| 21 31 structures evidence Interestingly, the 2 structures that have the largest tilt angle differences with the other variants, H3-23:L3-20 and H1-69:L3-20, have the smallest VH:VL interfaces, 684 and 725 Å2, respectively. RESULTS | |
| 54 76 tilt angle differences evidence Interestingly, the 2 structures that have the largest tilt angle differences with the other variants, H3-23:L3-20 and H1-69:L3-20, have the smallest VH:VL interfaces, 684 and 725 Å2, respectively. RESULTS | |
| 102 113 H3-23:L3-20 complex_assembly Interestingly, the 2 structures that have the largest tilt angle differences with the other variants, H3-23:L3-20 and H1-69:L3-20, have the smallest VH:VL interfaces, 684 and 725 Å2, respectively. RESULTS | |
| 118 129 H1-69:L3-20 complex_assembly Interestingly, the 2 structures that have the largest tilt angle differences with the other variants, H3-23:L3-20 and H1-69:L3-20, have the smallest VH:VL interfaces, 684 and 725 Å2, respectively. RESULTS | |
| 149 165 VH:VL interfaces site Interestingly, the 2 structures that have the largest tilt angle differences with the other variants, H3-23:L3-20 and H1-69:L3-20, have the smallest VH:VL interfaces, 684 and 725 Å2, respectively. RESULTS | |
| 0 11 H3-23:L3-20 complex_assembly H3-23:L3-20 is also unique in that it has the lowest value (0.676) of surface complementarity. RESULTS | |
| 70 93 surface complementarity evidence H3-23:L3-20 is also unique in that it has the lowest value (0.676) of surface complementarity. RESULTS | |
| 0 20 Melting temperatures evidence Melting temperatures for the 16 Fabs. TABLE | |
| 32 36 Fabs structure_element Melting temperatures for the 16 Fabs. TABLE | |
| 14 16 Tm evidence Colors: blue (Tm < 70°C), green (70°C < Tm < 73°C), yellow (73°C < Tm < 78°C), orange (Tm > 78°C). TABLE | |
| 40 42 Tm evidence Colors: blue (Tm < 70°C), green (70°C < Tm < 73°C), yellow (73°C < Tm < 78°C), orange (Tm > 78°C). TABLE | |
| 67 69 Tm evidence Colors: blue (Tm < 70°C), green (70°C < Tm < 73°C), yellow (73°C < Tm < 78°C), orange (Tm > 78°C). TABLE | |
| 87 89 Tm evidence Colors: blue (Tm < 70°C), green (70°C < Tm < 73°C), yellow (73°C < Tm < 78°C), orange (Tm > 78°C). TABLE | |
| 0 20 Melting temperatures evidence Melting temperatures (Tm) were measured for all Fabs using differential scanning calorimetry (Table 5). RESULTS | |
| 22 24 Tm evidence Melting temperatures (Tm) were measured for all Fabs using differential scanning calorimetry (Table 5). RESULTS | |
| 48 52 Fabs structure_element Melting temperatures (Tm) were measured for all Fabs using differential scanning calorimetry (Table 5). RESULTS | |
| 59 92 differential scanning calorimetry experimental_method Melting temperatures (Tm) were measured for all Fabs using differential scanning calorimetry (Table 5). RESULTS | |
| 31 33 LC structure_element It appears that for each given LC, the Fabs with germlines H1-69 and H3-23 are substantially more stable than those with germlines H3-53 and H5-51. RESULTS | |
| 39 43 Fabs structure_element It appears that for each given LC, the Fabs with germlines H1-69 and H3-23 are substantially more stable than those with germlines H3-53 and H5-51. RESULTS | |
| 59 64 H1-69 mutant It appears that for each given LC, the Fabs with germlines H1-69 and H3-23 are substantially more stable than those with germlines H3-53 and H5-51. RESULTS | |
| 69 74 H3-23 mutant It appears that for each given LC, the Fabs with germlines H1-69 and H3-23 are substantially more stable than those with germlines H3-53 and H5-51. RESULTS | |
| 98 104 stable protein_state It appears that for each given LC, the Fabs with germlines H1-69 and H3-23 are substantially more stable than those with germlines H3-53 and H5-51. RESULTS | |
| 131 136 H3-53 mutant It appears that for each given LC, the Fabs with germlines H1-69 and H3-23 are substantially more stable than those with germlines H3-53 and H5-51. RESULTS | |
| 141 146 H5-51 mutant It appears that for each given LC, the Fabs with germlines H1-69 and H3-23 are substantially more stable than those with germlines H3-53 and H5-51. RESULTS | |
| 13 18 L1-39 mutant In addition, L1-39 provides a much higher degree of stabilization than the other 3 LC germlines when combined with any of the HCs. RESULTS | |
| 83 85 LC structure_element In addition, L1-39 provides a much higher degree of stabilization than the other 3 LC germlines when combined with any of the HCs. RESULTS | |
| 126 129 HCs structure_element In addition, L1-39 provides a much higher degree of stabilization than the other 3 LC germlines when combined with any of the HCs. RESULTS | |
| 17 19 Tm evidence As a result, the Tm for pairs H1-69:L1-39 and H3-23:L1-39 is 12-13° higher than for pairs H3-53:L3-20, H3-53:L4-1, H5-51:L3-20 and H5-51:L4-1. RESULTS | |
| 30 41 H1-69:L1-39 complex_assembly As a result, the Tm for pairs H1-69:L1-39 and H3-23:L1-39 is 12-13° higher than for pairs H3-53:L3-20, H3-53:L4-1, H5-51:L3-20 and H5-51:L4-1. RESULTS | |
| 46 57 H3-23:L1-39 complex_assembly As a result, the Tm for pairs H1-69:L1-39 and H3-23:L1-39 is 12-13° higher than for pairs H3-53:L3-20, H3-53:L4-1, H5-51:L3-20 and H5-51:L4-1. RESULTS | |
| 90 101 H3-53:L3-20 complex_assembly As a result, the Tm for pairs H1-69:L1-39 and H3-23:L1-39 is 12-13° higher than for pairs H3-53:L3-20, H3-53:L4-1, H5-51:L3-20 and H5-51:L4-1. RESULTS | |
| 103 113 H3-53:L4-1 complex_assembly As a result, the Tm for pairs H1-69:L1-39 and H3-23:L1-39 is 12-13° higher than for pairs H3-53:L3-20, H3-53:L4-1, H5-51:L3-20 and H5-51:L4-1. RESULTS | |
| 115 126 H5-51:L3-20 complex_assembly As a result, the Tm for pairs H1-69:L1-39 and H3-23:L1-39 is 12-13° higher than for pairs H3-53:L3-20, H3-53:L4-1, H5-51:L3-20 and H5-51:L4-1. RESULTS | |
| 131 141 H5-51:L4-1 complex_assembly As a result, the Tm for pairs H1-69:L1-39 and H3-23:L1-39 is 12-13° higher than for pairs H3-53:L3-20, H3-53:L4-1, H5-51:L3-20 and H5-51:L4-1. RESULTS | |
| 89 107 crystal structures evidence These findings correlate well with the degree of conformational disorder observed in the crystal structures. RESULTS | |
| 9 12 CDR structure_element Parts of CDR H3 main chain are completely disordered, and were not modeled in Fabs H5-51:L3-20 and H5-51:L3-11 that have the lowest Tms in the set. RESULTS | |
| 13 15 H3 structure_element Parts of CDR H3 main chain are completely disordered, and were not modeled in Fabs H5-51:L3-20 and H5-51:L3-11 that have the lowest Tms in the set. RESULTS | |
| 42 52 disordered protein_state Parts of CDR H3 main chain are completely disordered, and were not modeled in Fabs H5-51:L3-20 and H5-51:L3-11 that have the lowest Tms in the set. RESULTS | |
| 78 82 Fabs structure_element Parts of CDR H3 main chain are completely disordered, and were not modeled in Fabs H5-51:L3-20 and H5-51:L3-11 that have the lowest Tms in the set. RESULTS | |
| 83 94 H5-51:L3-20 complex_assembly Parts of CDR H3 main chain are completely disordered, and were not modeled in Fabs H5-51:L3-20 and H5-51:L3-11 that have the lowest Tms in the set. RESULTS | |
| 99 110 H5-51:L3-11 complex_assembly Parts of CDR H3 main chain are completely disordered, and were not modeled in Fabs H5-51:L3-20 and H5-51:L3-11 that have the lowest Tms in the set. RESULTS | |
| 132 135 Tms evidence Parts of CDR H3 main chain are completely disordered, and were not modeled in Fabs H5-51:L3-20 and H5-51:L3-11 that have the lowest Tms in the set. RESULTS | |
| 3 19 electron density evidence No electron density is observed for a number of side chains in CDRs H3 and L3 in all Fabs with germline H3-53, which indicates loose packing of the variable domains. RESULTS | |
| 63 67 CDRs structure_element No electron density is observed for a number of side chains in CDRs H3 and L3 in all Fabs with germline H3-53, which indicates loose packing of the variable domains. RESULTS | |
| 68 70 H3 structure_element No electron density is observed for a number of side chains in CDRs H3 and L3 in all Fabs with germline H3-53, which indicates loose packing of the variable domains. RESULTS | |
| 75 77 L3 structure_element No electron density is observed for a number of side chains in CDRs H3 and L3 in all Fabs with germline H3-53, which indicates loose packing of the variable domains. RESULTS | |
| 85 89 Fabs structure_element No electron density is observed for a number of side chains in CDRs H3 and L3 in all Fabs with germline H3-53, which indicates loose packing of the variable domains. RESULTS | |
| 104 109 H3-53 mutant No electron density is observed for a number of side chains in CDRs H3 and L3 in all Fabs with germline H3-53, which indicates loose packing of the variable domains. RESULTS | |
| 148 164 variable domains structure_element No electron density is observed for a number of side chains in CDRs H3 and L3 in all Fabs with germline H3-53, which indicates loose packing of the variable domains. RESULTS | |
| 74 77 Tms evidence All those molecules are relatively unstable, as is reflected in their low Tms. RESULTS | |
| 30 65 systematic structural investigation experimental_method This is the first report of a systematic structural investigation of a phage germline library. DISCUSS | |
| 71 93 phage germline library experimental_method This is the first report of a systematic structural investigation of a phage germline library. DISCUSS | |
| 7 10 Fab structure_element The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 11 21 structures evidence The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 73 76 HCs structure_element The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 78 83 H1-69 mutant The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 85 90 H3-23 mutant The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 92 97 H3-53 mutant The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 103 108 H5-51 mutant The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 126 129 LCs structure_element The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 131 136 L1-39 mutant The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 138 143 L3-11 mutant The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 145 150 L3-20 mutant The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 155 159 L4-1 mutant The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 180 183 CDR structure_element The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 184 186 H3 structure_element The 16 Fab structures offer a unique look at all pairings of 4 different HCs (H1-69, H3-23, H3-53, and H5-51) and 4 different LCs (L1-39, L3-11, L3-20 and L4-1), all with the same CDR H3. DISCUSS | |
| 4 19 structural data evidence The structural data set taken as a whole provides insight into how the backbone conformations of the CDRs of a specific heavy or light chain vary when it is paired with 4 different light or heavy chains, respectively. DISCUSS | |
| 101 105 CDRs structure_element The structural data set taken as a whole provides insight into how the backbone conformations of the CDRs of a specific heavy or light chain vary when it is paired with 4 different light or heavy chains, respectively. DISCUSS | |
| 129 140 light chain structure_element The structural data set taken as a whole provides insight into how the backbone conformations of the CDRs of a specific heavy or light chain vary when it is paired with 4 different light or heavy chains, respectively. DISCUSS | |
| 190 202 heavy chains structure_element The structural data set taken as a whole provides insight into how the backbone conformations of the CDRs of a specific heavy or light chain vary when it is paired with 4 different light or heavy chains, respectively. DISCUSS | |
| 27 30 CDR structure_element A large variability in the CDR conformations for the sets of HCs and LCs is observed. DISCUSS | |
| 61 64 HCs structure_element A large variability in the CDR conformations for the sets of HCs and LCs is observed. DISCUSS | |
| 69 72 LCs structure_element A large variability in the CDR conformations for the sets of HCs and LCs is observed. DISCUSS | |
| 18 21 CDR structure_element In some cases the CDR conformations for all members of a set are virtually identical, for others subtle changes occur in a few members of a set, and in some cases larger deviations are observed within a set. DISCUSS | |
| 23 35 crystallized experimental_method The five variants that crystallized with 2 copies of the Fab in the asymmetric unit serve somewhat as controls for the influence of crystal packing on the conformations of the CDRs. DISCUSS | |
| 57 60 Fab structure_element The five variants that crystallized with 2 copies of the Fab in the asymmetric unit serve somewhat as controls for the influence of crystal packing on the conformations of the CDRs. DISCUSS | |
| 176 180 CDRs structure_element The five variants that crystallized with 2 copies of the Fab in the asymmetric unit serve somewhat as controls for the influence of crystal packing on the conformations of the CDRs. DISCUSS | |
| 17 27 structures evidence In four of the 5 structures the CDR conformations are consistent. DISCUSS | |
| 32 35 CDR structure_element In four of the 5 structures the CDR conformations are consistent. DISCUSS | |
| 26 37 H1-69:L3-20 complex_assembly In only one case, that of H1-69:L3-20 (the lowest resolution structure), do we see differences in the conformations of the 2 copies of CDRs H1 and L1. DISCUSS | |
| 61 70 structure evidence In only one case, that of H1-69:L3-20 (the lowest resolution structure), do we see differences in the conformations of the 2 copies of CDRs H1 and L1. DISCUSS | |
| 135 139 CDRs structure_element In only one case, that of H1-69:L3-20 (the lowest resolution structure), do we see differences in the conformations of the 2 copies of CDRs H1 and L1. DISCUSS | |
| 140 142 H1 structure_element In only one case, that of H1-69:L3-20 (the lowest resolution structure), do we see differences in the conformations of the 2 copies of CDRs H1 and L1. DISCUSS | |
| 147 149 L1 structure_element In only one case, that of H1-69:L3-20 (the lowest resolution structure), do we see differences in the conformations of the 2 copies of CDRs H1 and L1. DISCUSS | |
| 111 126 variable domain structure_element This variability is likely a result of 2 factors, crystal packing interactions and internal instability of the variable domain. DISCUSS | |
| 8 12 CDRs structure_element For the CDRs with canonical structures, the largest changes in conformation occur for CDR H1 of H1-69 and H3-53. DISCUSS | |
| 86 89 CDR structure_element For the CDRs with canonical structures, the largest changes in conformation occur for CDR H1 of H1-69 and H3-53. DISCUSS | |
| 90 92 H1 structure_element For the CDRs with canonical structures, the largest changes in conformation occur for CDR H1 of H1-69 and H3-53. DISCUSS | |
| 96 101 H1-69 mutant For the CDRs with canonical structures, the largest changes in conformation occur for CDR H1 of H1-69 and H3-53. DISCUSS | |
| 106 111 H3-53 mutant For the CDRs with canonical structures, the largest changes in conformation occur for CDR H1 of H1-69 and H3-53. DISCUSS | |
| 12 15 HCs structure_element The other 2 HCs, H3-23 and H5-51, have canonical structures that are remarkably well conserved (Fig. 1). DISCUSS | |
| 17 22 H3-23 mutant The other 2 HCs, H3-23 and H5-51, have canonical structures that are remarkably well conserved (Fig. 1). DISCUSS | |
| 27 32 H5-51 mutant The other 2 HCs, H3-23 and H5-51, have canonical structures that are remarkably well conserved (Fig. 1). DISCUSS | |
| 69 94 remarkably well conserved protein_state The other 2 HCs, H3-23 and H5-51, have canonical structures that are remarkably well conserved (Fig. 1). DISCUSS | |
| 9 12 HCs structure_element Of the 4 HCs, H1-69 has the greatest number of canonical structure assignments (Table 2). DISCUSS | |
| 14 19 H1-69 mutant Of the 4 HCs, H1-69 has the greatest number of canonical structure assignments (Table 2). DISCUSS | |
| 0 5 H1-69 mutant H1-69 is unique in having a pair of glycine residues at positions 26 and 27, which provide more conformational freedom in CDR H1. DISCUSS | |
| 36 43 glycine residue_name H1-69 is unique in having a pair of glycine residues at positions 26 and 27, which provide more conformational freedom in CDR H1. DISCUSS | |
| 66 68 26 residue_number H1-69 is unique in having a pair of glycine residues at positions 26 and 27, which provide more conformational freedom in CDR H1. DISCUSS | |
| 73 75 27 residue_number H1-69 is unique in having a pair of glycine residues at positions 26 and 27, which provide more conformational freedom in CDR H1. DISCUSS | |
| 96 118 conformational freedom protein_state H1-69 is unique in having a pair of glycine residues at positions 26 and 27, which provide more conformational freedom in CDR H1. DISCUSS | |
| 122 125 CDR structure_element H1-69 is unique in having a pair of glycine residues at positions 26 and 27, which provide more conformational freedom in CDR H1. DISCUSS | |
| 126 128 H1 structure_element H1-69 is unique in having a pair of glycine residues at positions 26 and 27, which provide more conformational freedom in CDR H1. DISCUSS | |
| 8 16 IGHV1-69 mutant Besides IGHV1-69, only the germlines of the VH4 family possess double glycines in CDR H1, and it will be interesting to see if they are also conformationally unstable. DISCUSS | |
| 44 47 VH4 structure_element Besides IGHV1-69, only the germlines of the VH4 family possess double glycines in CDR H1, and it will be interesting to see if they are also conformationally unstable. DISCUSS | |
| 70 78 glycines residue_name Besides IGHV1-69, only the germlines of the VH4 family possess double glycines in CDR H1, and it will be interesting to see if they are also conformationally unstable. DISCUSS | |
| 82 85 CDR structure_element Besides IGHV1-69, only the germlines of the VH4 family possess double glycines in CDR H1, and it will be interesting to see if they are also conformationally unstable. DISCUSS | |
| 86 88 H1 structure_element Besides IGHV1-69, only the germlines of the VH4 family possess double glycines in CDR H1, and it will be interesting to see if they are also conformationally unstable. DISCUSS | |
| 141 166 conformationally unstable protein_state Besides IGHV1-69, only the germlines of the VH4 family possess double glycines in CDR H1, and it will be interesting to see if they are also conformationally unstable. DISCUSS | |
| 14 19 VH:VL complex_assembly Having all 16 VH:VL pairs with the same CDR H3 provides some insights into why molecular modeling efforts of CDR H3 have proven so difficult. DISCUSS | |
| 40 43 CDR structure_element Having all 16 VH:VL pairs with the same CDR H3 provides some insights into why molecular modeling efforts of CDR H3 have proven so difficult. DISCUSS | |
| 44 46 H3 structure_element Having all 16 VH:VL pairs with the same CDR H3 provides some insights into why molecular modeling efforts of CDR H3 have proven so difficult. DISCUSS | |
| 109 112 CDR structure_element Having all 16 VH:VL pairs with the same CDR H3 provides some insights into why molecular modeling efforts of CDR H3 have proven so difficult. DISCUSS | |
| 113 115 H3 structure_element Having all 16 VH:VL pairs with the same CDR H3 provides some insights into why molecular modeling efforts of CDR H3 have proven so difficult. DISCUSS | |
| 69 73 Fabs structure_element As mentioned in the Results section, this data set is composed of 21 Fabs, since 5 of the 16 variants have 2 Fab copies in the asymmetric unit. DISCUSS | |
| 109 112 Fab structure_element As mentioned in the Results section, this data set is composed of 21 Fabs, since 5 of the 16 variants have 2 Fab copies in the asymmetric unit. DISCUSS | |
| 11 15 Fabs structure_element For the 18 Fabs with complete backbone atoms for CDR H3, 10 have conformations similar to that of the parent, while the others have significantly different conformations (Fig. 6). DISCUSS | |
| 49 52 CDR structure_element For the 18 Fabs with complete backbone atoms for CDR H3, 10 have conformations similar to that of the parent, while the others have significantly different conformations (Fig. 6). DISCUSS | |
| 53 55 H3 structure_element For the 18 Fabs with complete backbone atoms for CDR H3, 10 have conformations similar to that of the parent, while the others have significantly different conformations (Fig. 6). DISCUSS | |
| 28 31 CDR structure_element Thus, it is likely that the CDR H3 conformation is dependent upon 2 dominating factors: 1) amino acid sequence; and 2) VH and VL context. DISCUSS | |
| 32 34 H3 structure_element Thus, it is likely that the CDR H3 conformation is dependent upon 2 dominating factors: 1) amino acid sequence; and 2) VH and VL context. DISCUSS | |
| 119 121 VH structure_element Thus, it is likely that the CDR H3 conformation is dependent upon 2 dominating factors: 1) amino acid sequence; and 2) VH and VL context. DISCUSS | |
| 126 128 VL structure_element Thus, it is likely that the CDR H3 conformation is dependent upon 2 dominating factors: 1) amino acid sequence; and 2) VH and VL context. DISCUSS | |
| 103 108 VH:VL complex_assembly More than half of the variants retain the conformation of the parent despite having differences in the VH:VL pairing. DISCUSS | |
| 23 33 structures evidence This subset includes 2 structures with 2 copies of the Fab in the asymmetric unit, all of which are nearly identical in conformation. DISCUSS | |
| 55 58 Fab structure_element This subset includes 2 structures with 2 copies of the Fab in the asymmetric unit, all of which are nearly identical in conformation. DISCUSS | |
| 16 26 structures evidence The remaining 8 structures exhibit “non-parental” conformations, indicating that the VH and VL context can also be a dominating factor influencing CDR H3. DISCUSS | |
| 85 87 VH structure_element The remaining 8 structures exhibit “non-parental” conformations, indicating that the VH and VL context can also be a dominating factor influencing CDR H3. DISCUSS | |
| 92 94 VL structure_element The remaining 8 structures exhibit “non-parental” conformations, indicating that the VH and VL context can also be a dominating factor influencing CDR H3. DISCUSS | |
| 147 150 CDR structure_element The remaining 8 structures exhibit “non-parental” conformations, indicating that the VH and VL context can also be a dominating factor influencing CDR H3. DISCUSS | |
| 151 153 H3 structure_element The remaining 8 structures exhibit “non-parental” conformations, indicating that the VH and VL context can also be a dominating factor influencing CDR H3. DISCUSS | |
| 23 33 structures evidence This subset also has 2 structures with 2 Fab copies in the asymmetric unit. DISCUSS | |
| 41 44 Fab structure_element This subset also has 2 structures with 2 Fab copies in the asymmetric unit. DISCUSS | |
| 65 77 stem regions structure_element Interestingly, as described earlier, these 2 pairs differ in the stem regions with the H1-69:L3-20 pair in the ‘extended’ conformation and H5-51:L4-1 pair in the ‘kinked’ conformation. DISCUSS | |
| 87 98 H1-69:L3-20 complex_assembly Interestingly, as described earlier, these 2 pairs differ in the stem regions with the H1-69:L3-20 pair in the ‘extended’ conformation and H5-51:L4-1 pair in the ‘kinked’ conformation. DISCUSS | |
| 112 120 extended protein_state Interestingly, as described earlier, these 2 pairs differ in the stem regions with the H1-69:L3-20 pair in the ‘extended’ conformation and H5-51:L4-1 pair in the ‘kinked’ conformation. DISCUSS | |
| 139 149 H5-51:L4-1 complex_assembly Interestingly, as described earlier, these 2 pairs differ in the stem regions with the H1-69:L3-20 pair in the ‘extended’ conformation and H5-51:L4-1 pair in the ‘kinked’ conformation. DISCUSS | |
| 163 169 kinked protein_state Interestingly, as described earlier, these 2 pairs differ in the stem regions with the H1-69:L3-20 pair in the ‘extended’ conformation and H5-51:L4-1 pair in the ‘kinked’ conformation. DISCUSS | |
| 4 7 CDR structure_element The CDR H3 conformational analysis shows that, for each set of variants of one HC paired with the 4 different LCs, both “parental” and “non-parental” conformations are observed. DISCUSS | |
| 8 10 H3 structure_element The CDR H3 conformational analysis shows that, for each set of variants of one HC paired with the 4 different LCs, both “parental” and “non-parental” conformations are observed. DISCUSS | |
| 11 34 conformational analysis experimental_method The CDR H3 conformational analysis shows that, for each set of variants of one HC paired with the 4 different LCs, both “parental” and “non-parental” conformations are observed. DISCUSS | |
| 79 81 HC structure_element The CDR H3 conformational analysis shows that, for each set of variants of one HC paired with the 4 different LCs, both “parental” and “non-parental” conformations are observed. DISCUSS | |
| 110 113 LCs structure_element The CDR H3 conformational analysis shows that, for each set of variants of one HC paired with the 4 different LCs, both “parental” and “non-parental” conformations are observed. DISCUSS | |
| 74 76 LC structure_element The same variability is observed for the sets of variants composed of one LC paired with each of the 4 HCs. DISCUSS | |
| 103 106 HCs structure_element The same variability is observed for the sets of variants composed of one LC paired with each of the 4 HCs. DISCUSS | |
| 64 66 HC structure_element Thus, no patterns of conformational preference for a particular HC or LC emerge to shed any direct light on what drives the conformational differences. DISCUSS | |
| 70 72 LC structure_element Thus, no patterns of conformational preference for a particular HC or LC emerge to shed any direct light on what drives the conformational differences. DISCUSS | |
| 65 67 H3 structure_element This finding supports the hypothesis of Weitzner et al. that the H3 conformation is controlled both by its sequence and its environment. DISCUSS | |
| 49 59 tilt angle evidence In looking at a possible correlation between the tilt angle and the conformation of CDR H3, no clear trends are observed. DISCUSS | |
| 84 87 CDR structure_element In looking at a possible correlation between the tilt angle and the conformation of CDR H3, no clear trends are observed. DISCUSS | |
| 88 90 H3 structure_element In looking at a possible correlation between the tilt angle and the conformation of CDR H3, no clear trends are observed. DISCUSS | |
| 14 25 H1-69:L3-20 complex_assembly Two variants, H1-69:L3-20 and H3-23:L3-20, have the largest differences in the tilt angles compared to other variants as seen in Table 3. DISCUSS | |
| 30 41 H3-23:L3-20 complex_assembly Two variants, H1-69:L3-20 and H3-23:L3-20, have the largest differences in the tilt angles compared to other variants as seen in Table 3. DISCUSS | |
| 13 18 VH:VL complex_assembly The absolute VH:VL orientation parameters for the 2 Fabs (Table S2) show significant deviation in HL, LC1 and HC2 values (2-3 standard deviations from the mean). DISCUSS | |
| 19 41 orientation parameters evidence The absolute VH:VL orientation parameters for the 2 Fabs (Table S2) show significant deviation in HL, LC1 and HC2 values (2-3 standard deviations from the mean). DISCUSS | |
| 52 56 Fabs structure_element The absolute VH:VL orientation parameters for the 2 Fabs (Table S2) show significant deviation in HL, LC1 and HC2 values (2-3 standard deviations from the mean). DISCUSS | |
| 85 94 deviation evidence The absolute VH:VL orientation parameters for the 2 Fabs (Table S2) show significant deviation in HL, LC1 and HC2 values (2-3 standard deviations from the mean). DISCUSS | |
| 98 100 HL structure_element The absolute VH:VL orientation parameters for the 2 Fabs (Table S2) show significant deviation in HL, LC1 and HC2 values (2-3 standard deviations from the mean). DISCUSS | |
| 102 105 LC1 structure_element The absolute VH:VL orientation parameters for the 2 Fabs (Table S2) show significant deviation in HL, LC1 and HC2 values (2-3 standard deviations from the mean). DISCUSS | |
| 110 113 HC2 structure_element The absolute VH:VL orientation parameters for the 2 Fabs (Table S2) show significant deviation in HL, LC1 and HC2 values (2-3 standard deviations from the mean). DISCUSS | |
| 21 32 H3-23:L3-20 complex_assembly One of the variants, H3-23:L3-20, has the CDR H3 conformation similar to the parent, but the other, H1-69:L3-20, is different. DISCUSS | |
| 42 45 CDR structure_element One of the variants, H3-23:L3-20, has the CDR H3 conformation similar to the parent, but the other, H1-69:L3-20, is different. DISCUSS | |
| 46 48 H3 structure_element One of the variants, H3-23:L3-20, has the CDR H3 conformation similar to the parent, but the other, H1-69:L3-20, is different. DISCUSS | |
| 100 111 H1-69:L3-20 complex_assembly One of the variants, H3-23:L3-20, has the CDR H3 conformation similar to the parent, but the other, H1-69:L3-20, is different. DISCUSS | |
| 49 60 H1-69:L3-20 complex_assembly As noted in the Results section, the 2 variants, H1-69:L3-20 and H3-23:L3-20, are outliers in terms of the tilt angle; at the same time, both have the smallest VH:VL interface. DISCUSS | |
| 65 76 H3-23:L3-20 complex_assembly As noted in the Results section, the 2 variants, H1-69:L3-20 and H3-23:L3-20, are outliers in terms of the tilt angle; at the same time, both have the smallest VH:VL interface. DISCUSS | |
| 107 117 tilt angle evidence As noted in the Results section, the 2 variants, H1-69:L3-20 and H3-23:L3-20, are outliers in terms of the tilt angle; at the same time, both have the smallest VH:VL interface. DISCUSS | |
| 160 175 VH:VL interface site As noted in the Results section, the 2 variants, H1-69:L3-20 and H3-23:L3-20, are outliers in terms of the tilt angle; at the same time, both have the smallest VH:VL interface. DISCUSS | |
| 14 24 interfaces site These smaller interfaces may perhaps translate to a significant deviation in how VH is oriented relative to VL than the other variants. DISCUSS | |
| 81 83 VH structure_element These smaller interfaces may perhaps translate to a significant deviation in how VH is oriented relative to VL than the other variants. DISCUSS | |
| 108 110 VL structure_element These smaller interfaces may perhaps translate to a significant deviation in how VH is oriented relative to VL than the other variants. DISCUSS | |
| 76 81 VH:VL complex_assembly These deviations from the other variants can also be seen to some extent in VH:VL orientation parameters in Table S2, as well as in the smaller number of residues involved in the VH:VL interfaces of these 2 variants (Fig. S5). DISCUSS | |
| 179 195 VH:VL interfaces site These deviations from the other variants can also be seen to some extent in VH:VL orientation parameters in Table S2, as well as in the smaller number of residues involved in the VH:VL interfaces of these 2 variants (Fig. S5). DISCUSS | |
| 64 68 CDRs structure_element These differences undoubtedly influence the conformation of the CDRs, in particular CDR H1 (Fig. 1A) and CDR L1 (Fig. 3C), especially with the tandem glycines and multiple serines present, respectively. DISCUSS | |
| 84 87 CDR structure_element These differences undoubtedly influence the conformation of the CDRs, in particular CDR H1 (Fig. 1A) and CDR L1 (Fig. 3C), especially with the tandem glycines and multiple serines present, respectively. DISCUSS | |
| 88 90 H1 structure_element These differences undoubtedly influence the conformation of the CDRs, in particular CDR H1 (Fig. 1A) and CDR L1 (Fig. 3C), especially with the tandem glycines and multiple serines present, respectively. DISCUSS | |
| 105 108 CDR structure_element These differences undoubtedly influence the conformation of the CDRs, in particular CDR H1 (Fig. 1A) and CDR L1 (Fig. 3C), especially with the tandem glycines and multiple serines present, respectively. DISCUSS | |
| 109 111 L1 structure_element These differences undoubtedly influence the conformation of the CDRs, in particular CDR H1 (Fig. 1A) and CDR L1 (Fig. 3C), especially with the tandem glycines and multiple serines present, respectively. DISCUSS | |
| 150 158 glycines residue_name These differences undoubtedly influence the conformation of the CDRs, in particular CDR H1 (Fig. 1A) and CDR L1 (Fig. 3C), especially with the tandem glycines and multiple serines present, respectively. DISCUSS | |
| 172 179 serines residue_name These differences undoubtedly influence the conformation of the CDRs, in particular CDR H1 (Fig. 1A) and CDR L1 (Fig. 3C), especially with the tandem glycines and multiple serines present, respectively. DISCUSS | |
| 38 48 antibodies protein_type Pairing of different germlines yields antibodies with various degrees of stability. DISCUSS | |
| 20 40 melting temperatures evidence As indicated by the melting temperatures, germlines H1-69 and H3-23 for HC and germline L1-39 for LC produce more stable Fabs compared to the other germlines in the experimental set. DISCUSS | |
| 52 57 H1-69 mutant As indicated by the melting temperatures, germlines H1-69 and H3-23 for HC and germline L1-39 for LC produce more stable Fabs compared to the other germlines in the experimental set. DISCUSS | |
| 62 67 H3-23 mutant As indicated by the melting temperatures, germlines H1-69 and H3-23 for HC and germline L1-39 for LC produce more stable Fabs compared to the other germlines in the experimental set. DISCUSS | |
| 72 74 HC structure_element As indicated by the melting temperatures, germlines H1-69 and H3-23 for HC and germline L1-39 for LC produce more stable Fabs compared to the other germlines in the experimental set. DISCUSS | |
| 88 93 L1-39 mutant As indicated by the melting temperatures, germlines H1-69 and H3-23 for HC and germline L1-39 for LC produce more stable Fabs compared to the other germlines in the experimental set. DISCUSS | |
| 98 100 LC structure_element As indicated by the melting temperatures, germlines H1-69 and H3-23 for HC and germline L1-39 for LC produce more stable Fabs compared to the other germlines in the experimental set. DISCUSS | |
| 114 120 stable protein_state As indicated by the melting temperatures, germlines H1-69 and H3-23 for HC and germline L1-39 for LC produce more stable Fabs compared to the other germlines in the experimental set. DISCUSS | |
| 121 125 Fabs structure_element As indicated by the melting temperatures, germlines H1-69 and H3-23 for HC and germline L1-39 for LC produce more stable Fabs compared to the other germlines in the experimental set. DISCUSS | |
| 52 54 LC structure_element One possible explanation of the clear preference of LC germline L1-39 is that CDR L3 has smaller residues at positions 91 and 94, allowing for more room to accommodate CDR H3. DISCUSS | |
| 64 69 L1-39 mutant One possible explanation of the clear preference of LC germline L1-39 is that CDR L3 has smaller residues at positions 91 and 94, allowing for more room to accommodate CDR H3. DISCUSS | |
| 78 81 CDR structure_element One possible explanation of the clear preference of LC germline L1-39 is that CDR L3 has smaller residues at positions 91 and 94, allowing for more room to accommodate CDR H3. DISCUSS | |
| 82 84 L3 structure_element One possible explanation of the clear preference of LC germline L1-39 is that CDR L3 has smaller residues at positions 91 and 94, allowing for more room to accommodate CDR H3. DISCUSS | |
| 119 121 91 residue_number One possible explanation of the clear preference of LC germline L1-39 is that CDR L3 has smaller residues at positions 91 and 94, allowing for more room to accommodate CDR H3. DISCUSS | |
| 126 128 94 residue_number One possible explanation of the clear preference of LC germline L1-39 is that CDR L3 has smaller residues at positions 91 and 94, allowing for more room to accommodate CDR H3. DISCUSS | |
| 168 171 CDR structure_element One possible explanation of the clear preference of LC germline L1-39 is that CDR L3 has smaller residues at positions 91 and 94, allowing for more room to accommodate CDR H3. DISCUSS | |
| 172 174 H3 structure_element One possible explanation of the clear preference of LC germline L1-39 is that CDR L3 has smaller residues at positions 91 and 94, allowing for more room to accommodate CDR H3. DISCUSS | |
| 37 40 Tyr residue_name Other germlines have bulky residues, Tyr, Arg and Trp, at these positions, whereas L1-39 has Ser and Thr. DISCUSS | |
| 42 45 Arg residue_name Other germlines have bulky residues, Tyr, Arg and Trp, at these positions, whereas L1-39 has Ser and Thr. DISCUSS | |
| 50 53 Trp residue_name Other germlines have bulky residues, Tyr, Arg and Trp, at these positions, whereas L1-39 has Ser and Thr. DISCUSS | |
| 83 88 L1-39 mutant Other germlines have bulky residues, Tyr, Arg and Trp, at these positions, whereas L1-39 has Ser and Thr. DISCUSS | |
| 93 96 Ser residue_name Other germlines have bulky residues, Tyr, Arg and Trp, at these positions, whereas L1-39 has Ser and Thr. DISCUSS | |
| 101 104 Thr residue_name Other germlines have bulky residues, Tyr, Arg and Trp, at these positions, whereas L1-39 has Ser and Thr. DISCUSS | |
| 47 49 VL structure_element Various combinations of germline sequences for VL and VH impose certain constraints on CDR H3, which has to adapt to the environment. DISCUSS | |
| 54 56 VH structure_element Various combinations of germline sequences for VL and VH impose certain constraints on CDR H3, which has to adapt to the environment. DISCUSS | |
| 87 90 CDR structure_element Various combinations of germline sequences for VL and VH impose certain constraints on CDR H3, which has to adapt to the environment. DISCUSS | |
| 91 93 H3 structure_element Various combinations of germline sequences for VL and VH impose certain constraints on CDR H3, which has to adapt to the environment. DISCUSS | |
| 7 14 compact protein_state A more compact CDR L3 may be beneficial in this situation. DISCUSS | |
| 15 18 CDR structure_element A more compact CDR L3 may be beneficial in this situation. DISCUSS | |
| 19 21 L3 structure_element A more compact CDR L3 may be beneficial in this situation. DISCUSS | |
| 43 45 LC structure_element At the other end of the stability range is LC germline L3-20, which yields antibodies with the lowest Tms. DISCUSS | |
| 55 60 L3-20 mutant At the other end of the stability range is LC germline L3-20, which yields antibodies with the lowest Tms. DISCUSS | |
| 75 85 antibodies protein_type At the other end of the stability range is LC germline L3-20, which yields antibodies with the lowest Tms. DISCUSS | |
| 102 105 Tms evidence At the other end of the stability range is LC germline L3-20, which yields antibodies with the lowest Tms. DISCUSS | |
| 20 25 H3-53 mutant While pairings with H3-53 and H5-51 may be safely called a mismatch, those with H1-69 and H3-23 have Tms about 5-6° higher. DISCUSS | |
| 30 35 H5-51 mutant While pairings with H3-53 and H5-51 may be safely called a mismatch, those with H1-69 and H3-23 have Tms about 5-6° higher. DISCUSS | |
| 80 85 H1-69 mutant While pairings with H3-53 and H5-51 may be safely called a mismatch, those with H1-69 and H3-23 have Tms about 5-6° higher. DISCUSS | |
| 90 95 H3-23 mutant While pairings with H3-53 and H5-51 may be safely called a mismatch, those with H1-69 and H3-23 have Tms about 5-6° higher. DISCUSS | |
| 101 104 Tms evidence While pairings with H3-53 and H5-51 may be safely called a mismatch, those with H1-69 and H3-23 have Tms about 5-6° higher. DISCUSS | |
| 17 21 Fabs structure_element Curiously, the 2 Fabs, H1-69:L3-20 and H3-23:L3-20, deviate markedly in their tilt angles from the rest of the panel. DISCUSS | |
| 23 34 H1-69:L3-20 complex_assembly Curiously, the 2 Fabs, H1-69:L3-20 and H3-23:L3-20, deviate markedly in their tilt angles from the rest of the panel. DISCUSS | |
| 39 50 H3-23:L3-20 complex_assembly Curiously, the 2 Fabs, H1-69:L3-20 and H3-23:L3-20, deviate markedly in their tilt angles from the rest of the panel. DISCUSS | |
| 78 89 tilt angles evidence Curiously, the 2 Fabs, H1-69:L3-20 and H3-23:L3-20, deviate markedly in their tilt angles from the rest of the panel. DISCUSS | |
| 40 51 tilt angles evidence It is possible that by adopting extreme tilt angles the structure modulates CDR H3 and its environment, which apparently cannot be achieved solely by conformational rearrangement of the CDR. DISCUSS | |
| 56 65 structure evidence It is possible that by adopting extreme tilt angles the structure modulates CDR H3 and its environment, which apparently cannot be achieved solely by conformational rearrangement of the CDR. DISCUSS | |
| 76 79 CDR structure_element It is possible that by adopting extreme tilt angles the structure modulates CDR H3 and its environment, which apparently cannot be achieved solely by conformational rearrangement of the CDR. DISCUSS | |
| 80 82 H3 structure_element It is possible that by adopting extreme tilt angles the structure modulates CDR H3 and its environment, which apparently cannot be achieved solely by conformational rearrangement of the CDR. DISCUSS | |
| 186 189 CDR structure_element It is possible that by adopting extreme tilt angles the structure modulates CDR H3 and its environment, which apparently cannot be achieved solely by conformational rearrangement of the CDR. DISCUSS | |
| 22 37 VH:VL interface site Note that most of the VH:VL interface residues are invariant; therefore, significant change of the tilt angle must come with a penalty in free energy. DISCUSS | |
| 15 25 antibodies protein_type Yet, for the 2 antibodies, the total gain in stability merits the domain repacking. DISCUSS | |
| 30 33 Fab structure_element Overall, the stability of the Fab, as measured by Tm, is a result of the mutual adjustment of the HC and LC variable domains and adjustment of CDR H3 to the VH:VL cleft. DISCUSS | |
| 50 52 Tm evidence Overall, the stability of the Fab, as measured by Tm, is a result of the mutual adjustment of the HC and LC variable domains and adjustment of CDR H3 to the VH:VL cleft. DISCUSS | |
| 98 100 HC structure_element Overall, the stability of the Fab, as measured by Tm, is a result of the mutual adjustment of the HC and LC variable domains and adjustment of CDR H3 to the VH:VL cleft. DISCUSS | |
| 105 107 LC structure_element Overall, the stability of the Fab, as measured by Tm, is a result of the mutual adjustment of the HC and LC variable domains and adjustment of CDR H3 to the VH:VL cleft. DISCUSS | |
| 108 124 variable domains structure_element Overall, the stability of the Fab, as measured by Tm, is a result of the mutual adjustment of the HC and LC variable domains and adjustment of CDR H3 to the VH:VL cleft. DISCUSS | |
| 143 146 CDR structure_element Overall, the stability of the Fab, as measured by Tm, is a result of the mutual adjustment of the HC and LC variable domains and adjustment of CDR H3 to the VH:VL cleft. DISCUSS | |
| 147 149 H3 structure_element Overall, the stability of the Fab, as measured by Tm, is a result of the mutual adjustment of the HC and LC variable domains and adjustment of CDR H3 to the VH:VL cleft. DISCUSS | |
| 157 168 VH:VL cleft site Overall, the stability of the Fab, as measured by Tm, is a result of the mutual adjustment of the HC and LC variable domains and adjustment of CDR H3 to the VH:VL cleft. DISCUSS | |
| 167 176 structure evidence The final conformation represents an energetic minimum; however, in most cases it is very shallow, so that a single mutation can cause a dramatic rearrangement of the structure. DISCUSS | |
| 33 51 structural library experimental_method In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 100 103 HCs structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 109 112 LCs structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 132 135 CDR structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 136 138 H3 structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 173 181 antibody protein_type In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 182 191 structure evidence In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 276 278 L1 structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 280 282 L2 structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 284 286 L3 structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 288 290 H1 structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 295 297 H2 structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 298 302 CDRs structure_element In summary, the analysis of this structural library of germline variants composed of all pairs of 4 HCs and 4LCs, all with the same CDR H3, offers some unique insights into antibody structure and how pairing and sequence may influence, or not, the canonical structures of the L1, L2, L3, H1 and H2 CDRs. DISCUSS | |
| 18 21 CDR structure_element Comparison of the CDR H3s reveals a large set of variants with conformations similar to the parent, while a second set has significant conformational variability, indicating that both the sequence and the structural context define the CDR H3 conformation. DISCUSS | |
| 22 25 H3s structure_element Comparison of the CDR H3s reveals a large set of variants with conformations similar to the parent, while a second set has significant conformational variability, indicating that both the sequence and the structural context define the CDR H3 conformation. DISCUSS | |
| 235 238 CDR structure_element Comparison of the CDR H3s reveals a large set of variants with conformations similar to the parent, while a second set has significant conformational variability, indicating that both the sequence and the structural context define the CDR H3 conformation. DISCUSS | |
| 239 241 H3 structure_element Comparison of the CDR H3s reveals a large set of variants with conformations similar to the parent, while a second set has significant conformational variability, indicating that both the sequence and the structural context define the CDR H3 conformation. DISCUSS | |
| 39 50 H1-69:L3-20 complex_assembly Quite unexpectedly, 2 of the variants, H1-69:L3-20 and H3-53:L4-1, have the ‘extended’ stem region differing from the other 14 that have a ‘kinked’ stem region. DISCUSS | |
| 55 65 H3-53:L4-1 complex_assembly Quite unexpectedly, 2 of the variants, H1-69:L3-20 and H3-53:L4-1, have the ‘extended’ stem region differing from the other 14 that have a ‘kinked’ stem region. DISCUSS | |
| 77 85 extended protein_state Quite unexpectedly, 2 of the variants, H1-69:L3-20 and H3-53:L4-1, have the ‘extended’ stem region differing from the other 14 that have a ‘kinked’ stem region. DISCUSS | |
| 87 98 stem region structure_element Quite unexpectedly, 2 of the variants, H1-69:L3-20 and H3-53:L4-1, have the ‘extended’ stem region differing from the other 14 that have a ‘kinked’ stem region. DISCUSS | |
| 140 146 kinked protein_state Quite unexpectedly, 2 of the variants, H1-69:L3-20 and H3-53:L4-1, have the ‘extended’ stem region differing from the other 14 that have a ‘kinked’ stem region. DISCUSS | |
| 148 159 stem region structure_element Quite unexpectedly, 2 of the variants, H1-69:L3-20 and H3-53:L4-1, have the ‘extended’ stem region differing from the other 14 that have a ‘kinked’ stem region. DISCUSS | |
| 45 48 CDR structure_element These data reveal the difficulty of modeling CDR H3 accurately, as shown again in Antibody Modeling Assessment II. DISCUSS | |
| 49 51 H3 structure_element These data reveal the difficulty of modeling CDR H3 accurately, as shown again in Antibody Modeling Assessment II. DISCUSS | |
| 13 21 antibody protein_type Furthermore, antibody CDRs, H3 in particular, may go through conformational changes upon binding their targets, making structural prediction for docking purposes an even more difficult task. DISCUSS | |
| 22 26 CDRs structure_element Furthermore, antibody CDRs, H3 in particular, may go through conformational changes upon binding their targets, making structural prediction for docking purposes an even more difficult task. DISCUSS | |
| 28 30 H3 structure_element Furthermore, antibody CDRs, H3 in particular, may go through conformational changes upon binding their targets, making structural prediction for docking purposes an even more difficult task. DISCUSS | |
| 38 46 antibody protein_type Fortunately, for most applications of antibody modeling, such as engineering affinity and biophysical properties, an accurate CDR H3 structure is not always necessary. DISCUSS | |
| 126 129 CDR structure_element Fortunately, for most applications of antibody modeling, such as engineering affinity and biophysical properties, an accurate CDR H3 structure is not always necessary. DISCUSS | |
| 130 132 H3 structure_element Fortunately, for most applications of antibody modeling, such as engineering affinity and biophysical properties, an accurate CDR H3 structure is not always necessary. DISCUSS | |
| 133 142 structure evidence Fortunately, for most applications of antibody modeling, such as engineering affinity and biophysical properties, an accurate CDR H3 structure is not always necessary. DISCUSS | |
| 38 41 CDR structure_element For those applications where accurate CDR structures are essential, such as docking, the results in this work demonstrate the importance of experimental structures. DISCUSS | |
| 42 52 structures evidence For those applications where accurate CDR structures are essential, such as docking, the results in this work demonstrate the importance of experimental structures. DISCUSS | |
| 153 163 structures evidence For those applications where accurate CDR structures are essential, such as docking, the results in this work demonstrate the importance of experimental structures. DISCUSS | |
| 28 66 expression and crystallization methods experimental_method With the recent advances in expression and crystallization methods, Fab structures can be obtained rapidly. DISCUSS | |
| 68 71 Fab structure_element With the recent advances in expression and crystallization methods, Fab structures can be obtained rapidly. DISCUSS | |
| 72 82 structures evidence With the recent advances in expression and crystallization methods, Fab structures can be obtained rapidly. DISCUSS | |
| 23 26 Fab structure_element The set of 16 germline Fab structures offers a unique dataset to facilitate software development for antibody modeling. DISCUSS | |
| 27 37 structures evidence The set of 16 germline Fab structures offers a unique dataset to facilitate software development for antibody modeling. DISCUSS | |
| 101 109 antibody protein_type The set of 16 germline Fab structures offers a unique dataset to facilitate software development for antibody modeling. DISCUSS | |
| 65 75 structures evidence The results essentially support the underlying idea of canonical structures, indicating that most CDRs with germline sequences tend to adopt predefined conformations. DISCUSS | |
| 98 102 CDRs structure_element The results essentially support the underlying idea of canonical structures, indicating that most CDRs with germline sequences tend to adopt predefined conformations. DISCUSS | |
| 66 74 antibody protein_type From this point of view, a novel approach to design combinatorial antibody libraries would be to cover the range of CDR conformations that may not necessarily coincide with the germline usage in the human repertoire. DISCUSS | |
| 116 119 CDR structure_element From this point of view, a novel approach to design combinatorial antibody libraries would be to cover the range of CDR conformations that may not necessarily coincide with the germline usage in the human repertoire. DISCUSS | |
| 199 204 human species From this point of view, a novel approach to design combinatorial antibody libraries would be to cover the range of CDR conformations that may not necessarily coincide with the germline usage in the human repertoire. DISCUSS | |
| 80 90 antibodies protein_type This would insure more structural diversity, leading to a more diverse panel of antibodies that would bind to a broad spectrum of targets. DISCUSS | |